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Sample records for gen agxt r197q

  1. [Primary hiperoxaluria: a new mutation in gen AGXT (R197Q) cause of neonatal convulsions].

    PubMed

    Guevara-Campos, Jos; Riverol, Dbora; Gonzlez-Guevara, Luca; Tinedo, Rubin

    2008-12-01

    Primary hyperoxaluria is a congenital innate error of the metabolism of the amino acids, that is transmitted like an autosomal recessive character. Two types of hyperoxaluria exist: the primary type I, that corresponds to the peroxisomal enzymatic deficit of the alanine glyoxylate aminotransferase in the liver (AGT) and type II, due to the deficit of the glyoxylate reductase/hydroxypyruvate reductase deficiency (GRHPR). The primary type I (AGT) is the most frequenty. We report the case of a female infant of one month of age, that on her first day post birth, presented myoclonic convulsions and tonic spasms, both during wakefullness and sleep periods, that became more frequent and did not respond to the use of anticonvulsants. The ictal Electroencephalogram presented an intermittent activity of spikes and spike-waves of high voltage in the right hemisphere. Eight minutes after the intravenous administration of 150 mg of pyridoxine, it was observed a diminution of the epileptic activity, as well as the clinical manifestations. The determination of organic acids in urine revealed an increase in the concentration levels of oxalic acid (3064 mmol/mol of creatinine). The molecular genetic study of the AGXT gene, showed the existence of a R197Q mutation in exn 5 of the patient and her father. She received treatment with pyridoxine at a dose of 50 mg/day. When she reached the age of three months both a normal electroencephalogram and biochemistry were obtained. Although it is a rare cause of neonatal convulsions, hyperoxaluria, due to new mutations is an underdiagnosed disease by neonatologists and paediatricias. PMID:19245173

  2. AGXT2: a promiscuous aminotransferase

    PubMed Central

    Rodionov, Roman N.; Jarzebska, Natalia; Weiss, Norbert; Lentz, Steven R.

    2014-01-01

    Alanine-glyoxylate aminotransferase 2 (AGXT2) is a multifunctional mitochondrial aminotransferase that was first identified in 1978. The physiological importance of AGXT2 was largely overlooked for three decades because AGXT2 is less active in glyoxylate metabolism than AGXT1, the enzyme that is deficient in primary hyperoxaluria type I. Recently, several novel functions of AGXT2 have been “rediscovered” in the setting of modern genomic and metabolomic studies. It is now apparent that AGXT2 has multiple substrates and products and that altered AGXT2 activity may contribute to the pathogenesis of cardiovascular, renal, neurological and hematological diseases. This article reviews the biochemical properties and physiological functions of AGXT2, its unique role at the intersection of key mitochondrial pathways, and its potential as a drug target. PMID:25294000

  3. Identification of 5 novel mutations in the AGXT gene.

    PubMed

    Basmaison, O; Rolland, M O; Cochat, P; Bozon, D

    2000-06-01

    In order to identify additional genotypes in primary hyperoxaluria type 1, we sequenced the AGXT genes of 9 patients. We report 5 new mutations. Three are splice-site mutations situated at the end of intron 4 and 8 (647-1G>A, 969-1G>C, 969-3C>G), one is a missense mutation in exon 5 (D183N), and one is a short duplication in exon 2 (349ins7). Their consequence is always a lack of enzymatic activity of the Alanine-Glyoxylate Aminotransferase (AGT); for 4 of them, we were able to deduce that they were associated to the absence of AGT protein. These mutations are rare, as they have been found on one allele in our study (except 969-3C>G present in 2 unrelated families), and have not been previously reported. PMID:10862087

  4. Alanine-glyoxylate aminotransferase 2 (AGXT2) polymorphisms have considerable impact on methylarginine and ?-aminoisobutyrate metabolism in healthy volunteers.

    PubMed

    Kittel, Anja; Mller, Fabian; Knig, Jrg; Mieth, Maren; Sticht, Heinrich; Zolk, Oliver; Kralj, Ana; Heinrich, Markus R; Fromm, Martin F; Maas, Renke

    2014-01-01

    Elevated plasma concentrations of asymmetric (ADMA) and symmetric (SDMA) dimethylarginine have repeatedly been linked to adverse clinical outcomes. Both methylarginines are substrates of alanine-glyoxylate aminotransferase 2 (AGXT2). It was the aim of the present study to simultaneously investigate the functional relevance and relative contributions of common AGXT2 single nucleotide polymorphisms (SNPs) to plasma and urinary concentrations of methylarginines as well as ?-aminoisobutyrate (BAIB), a prototypic substrate of AGXT2. In a cohort of 400 healthy volunteers ADMA, SDMA and BAIB concentrations were determined in plasma and urine using HPLC-MS/MS and were related to the coding AGXT2 SNPs rs37369 (p.Val140Ile) and rs16899974 (p.Val498Leu). Volunteers heterozygous or homozygous for the AGXT2 SNP rs37369 had higher SDMA plasma concentrations by 5% and 20% (p?=?0.002) as well as higher BAIB concentrations by 54% and 146%, respectively, in plasma and 237% and 1661%, respectively, in urine (both p<0.001). ADMA concentrations were not affected by both SNPs. A haplotype analysis revealed that the second investigated AGXT2 SNP rs16899974, which was not significantly linked to the other AGXT2 SNP, further aggravates the effect of rs37369 with respect to BAIB concentrations in plasma and urine. To investigate the impact of the amino acid exchange p.Val140Ile, we established human embryonic kidney cell lines stably overexpressing wild-type or mutant (p.Val140Ile) AGXT2 protein and assessed enzyme activity using BAIB and stable-isotope labeled [H?]-SDMA as substrate. In vitro, the amino acid exchange of the mutant protein resulted in a significantly lower enzyme activity compared to wild-type AGXT2 (p<0.05). In silico modeling of the SNPs indicated reduced enzyme stability and substrate binding. In conclusion, SNPs of AGXT2 affect plasma as well as urinary BAIB and SDMA concentrations linking methylarginine metabolism to the common genetic trait of hyper-?-aminoisobutyric aciduria. PMID:24586340

  5. A double mutation in AGXT gene in families with primary hyperoxaluria type 1.

    PubMed

    Kanoun, Houda; Jarraya, Faial; Hadj Salem, Ikhlass; Mahfoudh, Hichem; Chaabouni, Yosr; Makni, Fatma; Hachicha, Jamil; Fakhfakh, Faiza

    2013-12-01

    Primary hyperoxaluria type 1 (PH1) is a severe autosomal recessive inherited disorder of glyoxylate metabolism caused by mutations in the AGXT gene on chromosome 2q37.3 that encodes the hepatic peroxisomal enzyme alanine:glyoxylate aminotransferase. These mutations are found throughout the entire gene and cause a wide spectrum of clinical severity. Rare in Europe, PH1 is responsible for 13% of the end stage renal failure in the Tunisian child. In the present work, we identified the double mutation c.32C>T (Pro11Leu) and c.731T>C (p.Ile244Thr) in AGXT gene in five unrelated Tunisian families with PH1 disease. Our results provide evidence regarding the potential involvement of c.32C>T, originally described as common polymorphism, on the resulting phenotype. We also reported an extreme intrafamilial heterogeneity in clinical presentation of PH1. Despite the same genetic background, the outcome of the affected members differs widely. The significant phenotypic heterogeneity observed within a same family, with a same genotype, suggests the existence of relevant modifier factors. PMID:24012869

  6. Alanine-glyoxylate aminotransferase 2 (AGXT2) Polymorphisms Have Considerable Impact on Methylarginine and β-aminoisobutyrate Metabolism in Healthy Volunteers

    PubMed Central

    König, Jörg; Mieth, Maren; Sticht, Heinrich; Zolk, Oliver; Kralj, Ana; Heinrich, Markus R.; Fromm, Martin F.; Maas, Renke

    2014-01-01

    Elevated plasma concentrations of asymmetric (ADMA) and symmetric (SDMA) dimethylarginine have repeatedly been linked to adverse clinical outcomes. Both methylarginines are substrates of alanine-glyoxylate aminotransferase 2 (AGXT2). It was the aim of the present study to simultaneously investigate the functional relevance and relative contributions of common AGXT2 single nucleotide polymorphisms (SNPs) to plasma and urinary concentrations of methylarginines as well as β-aminoisobutyrate (BAIB), a prototypic substrate of AGXT2. In a cohort of 400 healthy volunteers ADMA, SDMA and BAIB concentrations were determined in plasma and urine using HPLC-MS/MS and were related to the coding AGXT2 SNPs rs37369 (p.Val140Ile) and rs16899974 (p.Val498Leu). Volunteers heterozygous or homozygous for the AGXT2 SNP rs37369 had higher SDMA plasma concentrations by 5% and 20% (p = 0.002) as well as higher BAIB concentrations by 54% and 146%, respectively, in plasma and 237% and 1661%, respectively, in urine (both p<0.001). ADMA concentrations were not affected by both SNPs. A haplotype analysis revealed that the second investigated AGXT2 SNP rs16899974, which was not significantly linked to the other AGXT2 SNP, further aggravates the effect of rs37369 with respect to BAIB concentrations in plasma and urine. To investigate the impact of the amino acid exchange p.Val140Ile, we established human embryonic kidney cell lines stably overexpressing wild-type or mutant (p.Val140Ile) AGXT2 protein and assessed enzyme activity using BAIB and stable-isotope labeled [2H6]-SDMA as substrate. In vitro, the amino acid exchange of the mutant protein resulted in a significantly lower enzyme activity compared to wild-type AGXT2 (p<0.05). In silico modeling of the SNPs indicated reduced enzyme stability and substrate binding. In conclusion, SNPs of AGXT2 affect plasma as well as urinary BAIB and SDMA concentrations linking methylarginine metabolism to the common genetic trait of hyper-β-aminoisobutyric aciduria. PMID:24586340

  7. Primary hyperoxaluria type 1 and brachydactyly mental retardation syndrome caused by a novel mutation in AGXT and a terminal deletion of chromosome 2.

    PubMed

    Tammachote, Rachaneekorn; Kingsuwannapong, Nelawat; Tongkobpetch, Siraprapa; Srichomthong, Chalurmpon; Yeetong, Patra; Kingwatanakul, Pornchai; Monico, Carla G; Suphapeetiporn, Kanya; Shotelersuk, Vorasuk

    2012-09-01

    Primary hyperoxaluria type 1 (PH1) is an autosomal recessive disorder caused by mutations in the alanine:glyoxylate aminotransferase (AGXT) gene, located on chromosome 2q37. Mutant AGXT leads to excess production and excretion of oxalate, resulting in accumulation of calcium oxalate in the kidney, and progressive loss of renal function. Brachydactyly mental retardation syndrome (BDMR) is an autosomal dominant disorder, caused by haploinsufficiency of histone deacetylase 4 (HDAC4), also on chromosome 2q37. It is characterized by skeletal abnormalities and developmental delay. Here, we report on a girl who had phenotypes of both PH1 and BDMR. PCR-sequencing of the coding regions of AGXT showed a novel missense mutation, c.32C>G (p.Pro11Arg) inherited from her mother. Functional analyses demonstrated that it reduced the enzymatic activity to 31% of the wild-type and redirected some percentage of the enzyme away from the peroxisome. Microsatellite and array-CGH analyses indicated that the proband had a paternal de novo telomeric deletion of chromosome 2q, which included HDAC4. To our knowledge, this is the first report of PH1 and BDMR, with a novel AGXT mutation and a de novo telomeric deletion of chromosome 2q. PMID:22821680

  8. Partial deletion of the AGXT gene (EX1_EX7del): A new genotype in hyperoxaluria type 1.

    PubMed

    Nogueira, P K; Vuong, T S; Bouton, O; Maillard, A; Marchand, M; Rolland, M O; Cochat, P; Bozon, D

    2000-04-01

    Primary hyperoxaluria type 1 (PH1) is a rare autosomal (2q37.3) recessive metabolic disease caused by a deficiency of the hepatic peroxisomal enzyme alanine:glyoxylate amino transferase. Molecular heterogeneity is important in PH1 as most of the patients (if the parents are unrelated) are compound heterozygotes for rare mutations. We describe the first large deletion in the AGXT gene, removing exons 1 to 7 (EX1_EX7del) that was responsible for one case of severe PH1. This 10 kb deletion was identified by Southern blotting of genomic DNA digested by Xba I and hybridized with different exonic probes. Both parents (from Turkey) are first cousin and carry the deletion. It is of note that the presently reported patient did not exhibit any AGT catalytic activity and even so, he progressed towards end-stage renal disease only at 19 years old. PMID:10737993

  9. GenBank.

    PubMed

    Benson, D A; Boguski, M; Lipman, D J; Ostell, J

    1996-01-01

    The GenBank sequence database continues to expand its data coverage, quality control, annotation content and retrieval services. GenBank is comprised of DNA sequences submitted directly by authors as well as sequences from the other major public databases. An integrated retrieval system, known as Entrez, contains data from GenBank and from the major protein sequence and structural databases, as well as related MEDLINE abstracts. Users may access GenBank over the Internet through the World Wide Web and through special client-server programs for text and sequence similarity searching. FTP, CD-ROM and e-mail servers are alternate means of access. PMID:8594554

  10. GenBank.

    PubMed

    Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J; Ostell, James; Sayers, Eric W

    2016-01-01

    GenBank() (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species. Recent developments include a new starting page for submitters, a shift toward using accession.version identifiers rather than GI numbers, a wizard for submitting 16S rRNA sequences, and an Identical Protein Report to address growing issues of data redundancy. GenBank organizes the sequence data received from individual laboratories and large-scale sequencing projects into 18 divisions, and GenBank staff assign unique accession.version identifiers upon data receipt. Most submitters use the web-based BankIt or standalone Sequin programs. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the nuccore, nucest, and nucgss databases of the Entrez retrieval system, which integrates these records with a variety of other data including taxonomy nodes, genomes, protein structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:26590407

  11. GenBank: update

    PubMed Central

    Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

    2004-01-01

    GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps ensure worldwide coverage. GenBank is accessible through NCBIs retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:14681350

  12. GenBank

    PubMed Central

    Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Wheeler, David L.

    2003-01-01

    GenBank (R) is a comprehensive sequence database that contains publicly available DNA sequences for more than 119 000 different organisms, obtained primarily through the submission of sequence data from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin programs and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps ensure worldwide coverage. GenBank is accessible through NCBI's retrieval system, Entrez, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov. PMID:12519940

  13. GenBank

    PubMed Central

    Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2016-01-01

    GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species. Recent developments include a new starting page for submitters, a shift toward using accession.version identifiers rather than GI numbers, a wizard for submitting 16S rRNA sequences, and an Identical Protein Report to address growing issues of data redundancy. GenBank organizes the sequence data received from individual laboratories and large-scale sequencing projects into 18 divisions, and GenBank staff assign unique accession.version identifiers upon data receipt. Most submitters use the web-based BankIt or standalone Sequin programs. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the nuccore, nucest, and nucgss databases of the Entrez retrieval system, which integrates these records with a variety of other data including taxonomy nodes, genomes, protein structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:26590407

  14. Using GenBank.

    PubMed

    Sayers, Eric W; Karsch-Mizrachi, Ilene

    2016-01-01

    GenBank() is a comprehensive database of publicly available DNA sequences for 300,000 named organisms, more than 110,000 within the embryophyta, obtained through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Daily data exchange with the European Nucleotide Archive (ENA) in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases with taxonomy, genome, mapping, protein structure and domain information, as well as the biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. GenBank usage scenarios ranging from local analyses of the data available via FTP to online analyses supported by the NCBI web-based tools are discussed. To access GenBank and its related retrieval and analysis services, go to the NCBI home page at www.ncbi.nlm.nih.gov . PMID:26519398

  15. GenBank

    PubMed Central

    Benson, Dennis A.; Clark, Karen; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.

    2015-01-01

    GenBank (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. PMID:25414350

  16. GenBank.

    PubMed

    Benson, D A; Boguski, M; Lipman, D J; Ostell, J

    1994-09-01

    The GenBank sequence database continues to expand its data coverage, quality control, annotation content and retrieval services for the scientific community. Besides handling direct submissions of sequence data from authors, GenBank also incorporates DNA sequences from all available public sources; an integrated retrieval system, known as Entrez, also makes available data from the major protein sequence and structural databases, and from U.S. and European patents. MIDLINE abstracts from published articles describing the sequences are also included as an additional source of biological annotation for sequence entries. GenBank supports distribution of the data via FTP, CD-ROM, and E-mail servers. Network server-client programs provide access to an integrated database for literature retrieval and sequence similarity searching. PMID:7937042

  17. GenBank

    PubMed Central

    Burks, Christian; Cassidy, Maxxwell; Cinkosky, Michael J.; Cumella, Karen E.; Gilna, Paul; Hayden, Jamie E.-D.; Keen, Gifford M.; Kelley, Tom A.; Kelly, Michael; Kristofferson, David; Ryals, Julie

    1991-01-01

    The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 56,000,000 nucleotides in 45,000 entries. The input stream of data coming into the database has largely been shifted to direct submissions from the scientific community on electronic media. The data have been installed in a relational database management system and are made available in this form through on-line access, and through various network and off-line computer-readable media. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service. PMID:2041806

  18. Properties of Sin, Gen, and SinGen clusters

    NASA Astrophysics Data System (ADS)

    Dong, Yi; ur Rehman, Habib; Springborg, Michael

    2015-01-01

    The structures of Sin, Gen, and SinGen clusters with up to 44 atoms have been determined theoretically using an unbiased structure-optimization method in combination with a parametrized, density-functional description of the total energy for a given structure. By analyzing the total energy in detail, particularly stable clusters are identified. Moreover, general trends in the structures are identified with the help of specifically constructed descriptors.

  19. FutureGen Project Report

    SciTech Connect

    Cabe, Jim; Elliott, Mike

    2010-09-30

    This report summarizes the comprehensive siting, permitting, engineering, design, and costing activities completed by the FutureGen Industrial Alliance, the Department of Energy, and associated supporting subcontractors to develop a first of a kind near zero emissions integrated gasification combined cycle power plant and carbon capture and storage project (IGCC-CCS). With the goal to design, build, and reliably operate the first IGCC-CCS facility, FutureGen would have been the lowest emitting pulverized coal power plant in the world, while providing a timely and relevant basis for coal combustion power plants deploying carbon capture in the future. The content of this report summarizes key findings and results of applicable project evaluations; modeling, design, and engineering assessments; cost estimate reports; and schedule and risk mitigation from initiation of the FutureGen project through final flow sheet analyses including capital and operating reports completed under DOE award DE-FE0000587. This project report necessarily builds upon previously completed siting, design, and development work executed under DOE award DE-FC26- 06NT4207 which included the siting process; environmental permitting, compliance, and mitigation under the National Environmental Policy Act; and development of conceptual and design basis documentation for the FutureGen plant. For completeness, the report includes as attachments the siting and design basis documents, as well as the source documentation for the following: • Site evaluation and selection process and environmental characterization • Underground Injection Control (UIC) Permit Application including well design and subsurface modeling • FutureGen IGCC-CCS Design Basis Document • Process evaluations and technology selection via Illinois Clean Coal Review Board Technical Report • Process flow diagrams and heat/material balance for slurry-fed gasifier configuration • Process flow diagrams and heat/material balance for dry-fed gasifier configuration • Full capital cost report and cost category analysis (CAPEX) • Full operating cost report and assumptions (OPEX) Comparative technology evaluations, value engineering exercises, and initial air permitting activities are also provided; the report concludes with schedule, risk, and cost mitigation activities as well as lessons learned such that the products of this report can be used to support future investments in utility scale gasification and carbon capture and sequestration. Collectively, the FutureGen project enabled the comprehensive site specific evaluation and determination of the economic viability of IGCC-CCS. The project report is bound at that determination when DOE formally proposed the FutureGen 2.0 project which focuses on repowering a pulverized coal power plant with oxy-combustion technology including CCS.

  20. Summary of CPAS Gen II Parachute Analysis

    NASA Technical Reports Server (NTRS)

    Morris, Aaron L.; Bledsoe, Kristin J.; Fraire, Usbaldo, Jr.; Moore, James W.; Olson, Leah M.; Ray, Eric

    2011-01-01

    The Orion spacecraft is currently under development by NASA and Lockheed Martin. Like Apollo, Orion will use a series of parachutes to slow its descent and splashdown safely. The Orion parachute system, known as the CEV Parachute Assembly System (CPAS), is being designed by NASA, the Engineering and Science Contract Group (ESCG), and Airborne Systems. The first generation (Gen I) of CPAS testing consisted of thirteen tests and was executed in the 2007-2008 timeframe. The Gen I tests provided an initial understanding of the CPAS parachutes. Knowledge gained from Gen I testing was used to plan the second generation of testing (Gen II). Gen II consisted of six tests: three singleparachute tests, designated as Main Development Tests, and three Cluster Development Tests. Gen II required a more thorough investigation into parachute performance than Gen I. Higher fidelity instrumentation, enhanced analysis methods and tools, and advanced test techniques were developed. The results of the Gen II test series are being incorporated into the CPAS design. Further testing and refinement of the design and model of parachute performance will occur during the upcoming third generation of testing (Gen III). This paper will provide an overview of the developments in CPAS analysis following the end of Gen I, including descriptions of new tools and techniques as well as overviews of the Gen II tests.

  1. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend.

    PubMed

    Stackebrandt, E; Koch, C; Gvozdiak, O; Schumann, P

    1995-10-01

    The results of a phylogenetic and chemotaxonomic analysis of the genus Micrococcus indicated that it is significantly heterogeneous. Except for Micrococcus lylae, no species groups phylogenetically with the type species of the genus, Micrococcus luteus. The other members of the genus form three separate phylogenetic lines which on the basis of chemotaxonomic properties can be assigned to four genera. These genera are the genus Kocuria gen. nov. for Micrococcus roseus, Micrococcus varians, and Micrococcus kristinae, described as Kocuria rosea comb. nov., Kocuria varians comb. nov., and Kocuria kristinae comb. nov., respectively; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Nesterenkonia gen. nov. for Micrococcus halobius, described as Nesterenkonia halobia comb. nov.; the genus Dermacoccus gen. nov. for Micrococcus nishinomiyaensis, described as Dermacoccus nishinomiyaensis comb. nov.; and the genus Kytocossus gen. nov. for Micrococcus sedentarius, described as Kytococcus sedentarius comb. nov. M. luteus and M. lylae, which are closely related phylogenetically but differ in some chemotaxonomic properties, are the only species that remain in the genus Micrococcus Cohn 1872. An emended description of the genus Micrococcus is given [corrected]. PMID:7547287

  2. AutoGen Version 5.0

    NASA Technical Reports Server (NTRS)

    Gladden, Roy E.; Khanampornpan, Teerapat; Fisher, Forest W.

    2010-01-01

    Version 5.0 of the AutoGen software has been released. Previous versions, variously denoted Autogen and autogen, were reported in two articles: Automated Sequence Generation Process and Software (NPO-30746), Software Tech Briefs (Special Supplement to NASA Tech Briefs), September 2007, page 30, and Autogen Version 2.0 (NPO- 41501), NASA Tech Briefs, Vol. 31, No. 10 (October 2007), page 58. To recapitulate: AutoGen (now signifying automatic sequence generation ) automates the generation of sequences of commands in a standard format for uplink to spacecraft. AutoGen requires fewer workers than are needed for older manual sequence-generation processes, and greatly reduces sequence-generation times. The sequences are embodied in spacecraft activity sequence files (SASFs). AutoGen automates generation of SASFs by use of another previously reported program called APGEN. AutoGen encodes knowledge of different mission phases and of how the resultant commands must differ among the phases. AutoGen also provides means for customizing sequences through use of configuration files. The approach followed in developing AutoGen has involved encoding the behaviors of a system into a model and encoding algorithms for context-sensitive customizations of the modeled behaviors. This version of AutoGen addressed the MRO (Mars Reconnaissance Orbiter) primary science phase (PSP) mission phase. On previous Mars missions this phase has more commonly been referred to as mapping phase. This version addressed the unique aspects of sequencing orbital operations and specifically the mission specific adaptation of orbital operations for MRO. This version also includes capabilities for MRO s role in Mars relay support for UHF relay communications with the MER rovers and the Phoenix lander.

  3. Unleashing Gen Y: Marketing Mars to Millennials

    NASA Technical Reports Server (NTRS)

    Leahy, Bart D.; Hidalgo, Loretta; Kloberdanz, Cassie

    2007-01-01

    Space advocates need to engage Generation Y (born 1977-1999).This outreach is necessary to recruit the next generation of scientists and engineers to explore Mars. Space advocates in the non-profit, private, and government sectors need to use a combination of technical communication, marketing, and politics, to develop messages that resonate with Gen Y. Until now, space messages have been generated by and for college-educated white males; Gen Y is much more diverse, including as much as one third minorities. Young women, too, need to be reached. My research has shown that messages emphasizing technology, fun, humor, and opportunity are the best means of reaching the Gen Y audience of 60 million (US population is 300 million). The important things space advocates must avoid are talking down to this generation, making false promises, or expecting them to "wait their turn" before they can participate. This is the MTV generation! We need to find ways of engaging Gen Y now to build a future where human beings can live and work on the planet Mars. In addition to the messages themselves, advocates need to keep up with Gen Y' s social networking and use of iPods, cell phones, and the Internet. NASA and space advocacy groups can use these tools for "viral marketing," where young people share targeted space-related information via cell phones or the Internet because they like it. Overall, Gen Y is a socially dynamic and media-savvy group; advocates' space messages need to be sincere, creative, and placed in locations where Gen Y lives. Mars messages must be memorable!

  4. VIEW OF GEN. LOGAN STATUE LOOKING SOUTHWEST WITH VISTA AS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF GEN. LOGAN STATUE LOOKING SOUTHWEST WITH VISTA AS TO THE GEN. THOMAS STATUE DOWN VERMONT AVENUE AND THE GEN. SCOTT STATUE DOWN RHODE ISLAND AVENUE IN THE BACKGROUND - Logan Circle, Vermont Avenue, Rhode Island Avenue, & Thirteenth Street, Washington, District of Columbia, DC

  5. 75 FR 54221 - RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-03

    ... Federal Aviation Administration RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice of RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  6. 78 FR 8108 - NextGen Solutions Vendors Guide

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-05

    ... International Trade Administration NextGen Solutions Vendors Guide AGENCY: International Trade Administration... Transportation System (NextGen) solutions that meet the requirements of the International Civil Aviation Organization's (ICAO) Aviation System Block Upgrade (ASBU) initiative. The NextGen solutions address the...

  7. 77 FR 2342 - Fifth Meeting: RTCA, Next Gen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-17

    ... TRANSPORTATION Federal Aviation Administration Fifth Meeting: RTCA, Next Gen Advisory Committee AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA, NextGen... RTCA, NextGen Advisory Committee. DATES: The meeting will be held February 3, 2012, from 9:30...

  8. The Integrated Airport: Building a Successful NextGen Testbed

    SciTech Connect

    Frederick-Recascino, Christina; Sweigard, Doug; Lester, Wade

    2009-02-18

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment. NextGen refers to the program that will be initiated to modernize the US National Airspace. As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success. This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation.

  9. The Integrated Airport: Building a Successful NextGen Testbed

    SciTech Connect

    Frederick-Recascino, Christina; Sweigard, Doug; Lester, Wade

    2009-02-18

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment. NextGen refers to the program that will be initiated to modernize the US National Airspace. As with any major, multi-decadeinitiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success. This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation.

  10. Apoptosis in infectious mononucleosis: its detection with the Beckman Coulter GenS hematology analyzer.

    PubMed

    Aulesa, C; Prieto, M; Pinadero, M; Mainar, I

    2005-01-01

    This article describes the potential of the Beckman Coulter GenS hematology analyzer for detecting and quantifying the phenomenon of elevated apoptosis found during the incubation at 37 degrees C of samples containing CD45RO+ reactive T-lymphocytes from patients with infectious mononucleosis (IM). Visual detection was carried out with the GenS DF1 scattergram (volume/scatter), and the means and SDs of lymphocyte positional parameters (volume, scatter, and conductivity) were recorded from the instrument research screen before and after samples were incubated in an oven for 4 hours. Thirty-one IM samples were analyzed, and the results obtained after sample incubation showed a mean reduction in lymphocyte volume of 34%, a 3.9% increase in scatter, and a 4% increase in conductivity. A new cluster of cells consistent with apoptotic lymphocytes appeared in the GenS DF1 scattergram. May-Gr-Giemsa staining and extended manual counting of the samples carried out at the same time to validate and quantify the apoptosis of the analyzed samples detected a significant increase in apoptotic cells from 1.2% (range, 0%-3%) to 8.37% (range, 1%-39%) after incubation. The same process was used to evaluate a control group of patients, and the possible interference of platelet aggregation and erythroblasts (nucleated red blood cells) in GenS apoptosis quantification was investigated. The final results showed that the appearance of the apoptotic cluster in the GenS DF1 scattergram occurred in 96.8% of the IM cases, although this phenomenon is apparently nonspecific because similar clusters appear in other pathologies, such as viral infections (hepatitis, cytomegalovirus, and acquired immune deficiency syndrome). Additional quantitative studies of apoptosis kinetics indicated that at least 4 hours of incubation are necessary. This finding has directed an investigation of apoptosis-inducing drugs (camptothecin, theophylline) to reduce incubation time and thereby enhance the practical application of automated apoptosis detection in the diagnosis of IM and other diseases in which the phenomenon of apoptosis occurs. PMID:15790546

  11. Gen IV Materials Handbook Implementation Plan

    SciTech Connect

    Rittenhouse, P.; Ren, W.

    2005-03-29

    A Gen IV Materials Handbook is being developed to provide an authoritative single source of highly qualified structural materials information and materials properties data for use in design and analyses of all Generation IV Reactor Systems. The Handbook will be responsive to the needs expressed by all of the principal government, national laboratory, and private company stakeholders of Gen IV Reactor Systems. The Gen IV Materials Handbook Implementation Plan provided here addresses the purpose, rationale, attributes, and benefits of the Handbook and will detail its content, format, quality assurance, applicability, and access. Structural materials, both metallic and ceramic, for all Gen IV reactor types currently supported by the Department of Energy (DOE) will be included in the Gen IV Materials Handbook. However, initial emphasis will be on materials for the Very High Temperature Reactor (VHTR). Descriptive information (e.g., chemical composition and applicable technical specifications and codes) will be provided for each material along with an extensive presentation of mechanical and physical property data including consideration of temperature, irradiation, environment, etc. effects on properties. Access to the Gen IV Materials Handbook will be internet-based with appropriate levels of control. Information and data in the Handbook will be configured to allow search by material classes, specific materials, specific information or property class, specific property, data parameters, and individual data points identified with materials parameters, test conditions, and data source. Details on all of these as well as proposed applicability and consideration of data quality classes are provided in the Implementation Plan. Website development for the Handbook is divided into six phases including (1) detailed product analysis and specification, (2) simulation and design, (3) implementation and testing, (4) product release, (5) project/product evaluation, and (6) product maintenance and enhancement. Contracting of development of the Handbook website is discussed in terms of host server options, cost, technology, developer background and cooperative nature, and company stability. One of the first and most important activities in website development will be the generation of a detailed Handbook product requirements document including case diagrams and functional requirements tables. The Implementation Plan provides a detailed overview of the organizational structure of the Handbook and details of Handbook preparation, publication, and distribution. Finally, the Implementation Plan defines Quality Assurance requirements for the Handbook.

  12. Safety Assurance in NextGen

    NASA Technical Reports Server (NTRS)

    HarrisonFleming, Cody; Spencer, Melissa; Leveson, Nancy; Wilkinson, Chris

    2012-01-01

    The generation of minimum operational, safety, performance, and interoperability requirements is an important aspect of safely integrating new NextGen components into the Communication Navigation Surveillance and Air Traffic Management (CNS/ATM) system. These requirements are used as part of the implementation and approval processes. In addition, they provide guidance to determine the levels of design assurance and performance that are needed for each element of the new NextGen procedures, including aircraft, operator, and Air Navigation and Service Provider. Using the enhanced Airborne Traffic Situational Awareness for InTrail Procedure (ATSA-ITP) as an example, this report describes some limitations of the current process used for generating safety requirements and levels of required design assurance. An alternative process is described, as well as the argument for why the alternative can generate more comprehensive requirements and greater safety assurance than the current approach.

  13. GEN3D Ver. 1.37

    SciTech Connect

    2012-01-04

    GEN3D is a three-dimensional mesh generation program. The three-dimensional mesh is generated by mapping a two-dimensional mesh into threedimensions according to one of four types of transformations: translating, rotating, mapping onto a spherical surface, and mapping onto a cylindrical surface. The generated three-dimensional mesh can then be reoriented by offsetting, reflecting about an axis, and revolving about an axis. GEN3D can be used to mesh geometries that are axisymmetric or planar, but, due to three-dimensional loading or boundary conditions, require a three-dimensional finite element mesh and analysis. More importantly, it can be used to mesh complex three-dimensional geometries composed of several sections when the sections can be defined in terms of transformations of two dimensional geometries. The code GJOIN is then used to join the separate sections into a single body. GEN3D reads and writes twodimensional and threedimensional mesh databases in the GENESIS database format; therefore, it is compatible with the preprocessing, postprocessing, and analysis codes used by the Engineering Analysis Department at Sandia National Laboratories, Albuquerque, NM.

  14. Complications Following BellaGen Injection

    PubMed Central

    Park, Mi Kyung; Kim, Hyun Kyu; Park, Kui Young; Li, Kapsok; Hong, Chang Kwun

    2011-01-01

    BellaGen is an injectable acellular dermal matrix granule derived from donated human skin tissue that was recently developed for soft tissue augmentation. Its use has been sporadically reported in penile girth enhancement procedures. Many cases of complications have been reported after injecting acellular dermal matrices like AlloDerm or SureDerm but few reports on complications associated with BellaGen injection. We report here on penile skin inflammation and necrosis following augmentation phalloplasty with BellaGen, which developed 3 days after the injection and persisted for more than 2 weeks. The patient had a 15 year history of type 2 diabetes mellitus, and he was treated with oral antibiotics and wet dressings with KMNO4 solution to combine preservation of the remaining penile soft tissue with debridement of avascular tissue. The lesion improved with this treatment, but the patient experienced pain for about 2 weeks. All patients should be informed of the potential complications with the use of injectable acellular dermal matrices before treatment. Patient selection for augmentation is also important to have the most desirable results. PMID:22346264

  15. GEN3D Ver. 1.37

    Energy Science and Technology Software Center (ESTSC)

    2012-01-04

    GEN3D is a three-dimensional mesh generation program. The three-dimensional mesh is generated by mapping a two-dimensional mesh into threedimensions according to one of four types of transformations: translating, rotating, mapping onto a spherical surface, and mapping onto a cylindrical surface. The generated three-dimensional mesh can then be reoriented by offsetting, reflecting about an axis, and revolving about an axis. GEN3D can be used to mesh geometries that are axisymmetric or planar, but, due to three-dimensionalmore » loading or boundary conditions, require a three-dimensional finite element mesh and analysis. More importantly, it can be used to mesh complex three-dimensional geometries composed of several sections when the sections can be defined in terms of transformations of two dimensional geometries. The code GJOIN is then used to join the separate sections into a single body. GEN3D reads and writes twodimensional and threedimensional mesh databases in the GENESIS database format; therefore, it is compatible with the preprocessing, postprocessing, and analysis codes used by the Engineering Analysis Department at Sandia National Laboratories, Albuquerque, NM.« less

  16. TidGen Power System Commercialization Project

    SciTech Connect

    Sauer, Christopher R.; McEntee, Jarlath

    2013-12-30

    ORPC Maine, LLC, a wholly-owned subsidiary of Ocean Renewable Power Company, LLC (collectively ORPC), submits this Final Technical Report for the TidGen® Power System Commercialization Project (Project), partially funded by the U.S. Department of Energy (DE-EE0003647). The Project was built and operated in compliance with the Federal Energy Regulatory Commission (FERC) pilot project license (P-12711) and other permits and approvals needed for the Project. This report documents the methodologies, activities and results of the various phases of the Project, including design, engineering, procurement, assembly, installation, operation, licensing, environmental monitoring, retrieval, maintenance and repair. The Project represents a significant achievement for the renewable energy portfolio of the U.S. in general, and for the U.S. marine hydrokinetic (MHK) industry in particular. The stated Project goal was to advance, demonstrate and accelerate deployment and commercialization of ORPC’s tidal-current based hydrokinetic power generation system, including the energy extraction and conversion technology, associated power electronics, and interconnection equipment capable of reliably delivering electricity to the domestic power grid. ORPC achieved this goal by designing, building and operating the TidGen® Power System in 2012 and becoming the first federally licensed hydrokinetic tidal energy project to deliver electricity to a power grid under a power purchase agreement in North America. Located in Cobscook Bay between Eastport and Lubec, Maine, the TidGen® Power System was connected to the Bangor Hydro Electric utility grid at an on-shore station in North Lubec on September 13, 2012. ORPC obtained a FERC pilot project license for the Project on February 12, 2012 and the first Maine Department of Environmental Protection General Permit issued for a tidal energy project on January 31, 2012. In addition, ORPC entered into a 20-year agreement with Bangor Hydro Electric Company on January 1, 2013 for up to 5 megawatts at a price of $215/MWh, escalating at 2.0% per year.

  17. Gen IV Materials Handbook Functionalities and Operation

    SciTech Connect

    Ren, Weiju

    2009-12-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  18. Towards an International Culture: Gen Y Students and SNS?

    ERIC Educational Resources Information Center

    Lichy, Jessica

    2012-01-01

    This article reports the findings of a small-scale investigation into the Internet user behaviour of generation Y (Gen Y) students, with particular reference to social networking sites. The study adds to the literature on cross-cultural Internet user behaviour with specific reference to Gen Y and social networking. It compares how a cohort of…

  19. Towards an International Culture: Gen Y Students and SNS?

    ERIC Educational Resources Information Center

    Lichy, Jessica

    2012-01-01

    This article reports the findings of a small-scale investigation into the Internet user behaviour of generation Y (Gen Y) students, with particular reference to social networking sites. The study adds to the literature on cross-cultural Internet user behaviour with specific reference to Gen Y and social networking. It compares how a cohort of

  20. Hoja informativa de pruebas genéticas

    Cancer.gov

    Trata de pruebas genéticas para riesgos heredados de cáncer; incluye tipos de pruebas, para quién son, explicación y confidencialidad de los resultados. Ofrece información de pruebas genéticas a domicilio o pruebas para el consumidor.

  1. The Integrated Airport: Building a Successful NextGen Testbed

    ScienceCinema

    Frederick-Recascino, Christina [Embry-Riddle Aeronautical University, Daytona Beach, Florida, United States]; Sweigard, Doug [Lockheed Martin Corporation]; Lester, Wade [ERAU

    2010-01-08

    This presentation will describe a unique public-private partnership - the Integrated Airport - that was created to engage in research and testing related to NextGen Technology deployment.  NextGen refers to the program that will be initiated to modernize the US National Airspace.  As with any major, multi-decade initiative, such as NextGen, integration of work efforts by multiple partners in the modernization is critical for success.  This talk will focus on the development of the consortium, how the consortium plans for NextGen initiatives, the series of technology demonstrations we have produced and plans for the future of NextGen testing and implementation. 

  2. Back to the FutureGen?

    SciTech Connect

    Buchsbaum, L.

    2009-04-15

    After years of political wrangling, Democrats may green-light the experimental clean coal power plants. The article relates how the project came to be curtailed, how Senator Dick Durbin managed to protect $134 million in funding for FutureGen in Mattoon, and how once Obama was in office a $2 billion line item to fund a 'near zero emissions power plant(s)' was placed in the Senate version of the Stimulus Bill. The final version of the legislation cut the funding to $1 billion for 'fossil energy research and development'. In December 2008 the FutureGen Alliance and the City of Mattoon spent $6.5 billion to purchase the plants eventual 440 acre site. A report by the Government Accountability Office (GAO) said that Bush's inaction may have set back clean coal technology in the US by as much as a decade. If additional funding comes through construction of the plant could start in 2010. 1 fig., 1 photo.

  3. Head-worn displays for NextGen

    NASA Astrophysics Data System (ADS)

    Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J., III

    2011-06-01

    The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

  4. RxGen General Optical Model Prescription Generator

    NASA Technical Reports Server (NTRS)

    Sigrist, Norbert

    2012-01-01

    RxGen is a prescription generator for JPL's in-house optical modeling software package called MACOS (Modeling and Analysis for Controlled Optical Systems), which is an expert optical analysis software package focusing on modeling optics on dynamic structures, deformable optics, and controlled optics. The objectives of RxGen are to simplify and automate MACOS prescription generations, reducing errors associated with creating such optical prescriptions, and improving user efficiency without requiring MACOS proficiency. RxGen uses MATLAB (a high-level language and interactive environment developed by MathWorks) as the development and deployment platform, but RxGen can easily be ported to another optical modeling/analysis platform. Running RxGen within the modeling environment has the huge benefit that variations in optical models can be made an integral part of the modeling state. For instance, optical prescription parameters determined as external functional dependencies, optical variations by controlling the in-/exclusion of optical components like sub-systems, and/or controlling the state of all components. Combining the mentioned capabilities and flexibilities with RxGen's optical abstraction layer completely eliminates the hindering aspects for requiring proficiency in writing/editing MACOS prescriptions, allowing users to focus on the modeling aspects of optical systems, i.e., increasing productivity and efficiency. RxGen provides significant enhancements to MACOS and delivers a framework for fast prototyping as well as for developing very complex controlled optical systems.

  5. Head-Worn Displays for NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Shelton, Kevin J.; Arthur, J. J.

    2011-01-01

    The operating concepts emerging under the Next Generation air transportation system (NextGen) require new technology and procedures - not only on the ground-side - but also on the flight deck. Flight deck display and decision support technologies are specifically targeted to overcome aircraft safety barriers that might otherwise constrain the full realization of NextGen. One such technology is the very lightweight, unobtrusive head-worn display (HWD). HWDs with an integrated head-tracking system are being researched as they offer significant potential benefit under emerging NextGen operational concepts. Two areas of benefit for NextGen are defined. First, the HWD may be designed to be equivalent to the Head-Up Display (HUD) using Virtual HUD concepts. As such, these operational credits may be provided to significantly more aircraft for which HUD installation is neither practical nor possible. Second, the HWD provides unique display capabilities, such as an unlimited field-of-regard. These capabilities may be integral to emerging NextGen operational concepts, eliminating safety issues which might otherwise constrain the full realization of NextGen. The paper details recent research results, current HWD technology limitations, and future technology development needed to realize HWDs as a enabling technology for NextGen.

  6. NextGen Future Safety Assessment Game

    NASA Technical Reports Server (NTRS)

    Ancel, Ersin; Gheorghe, Adian; Jones, Sharon Monica

    2010-01-01

    The successful implementation of the next generation infrastructure systems requires solid understanding of their technical, social, political and economic aspects along with their interactions. The lack of historical data that relate to the long-term planning of complex systems introduces unique challenges for decision makers and involved stakeholders which in turn result in unsustainable systems. Also, the need to understand the infrastructure at the societal level and capture the interaction between multiple stakeholders becomes important. This paper proposes a methodology in order to develop a holistic approach aiming to provide an alternative subject-matter expert (SME) elicitation and data collection method for future sociotechnical systems. The methodology is adapted to Next Generation Air Transportation System (NextGen) decision making environment in order to demonstrate the benefits of this holistic approach.

  7. The GenDev Curriculum Development Workshop.

    PubMed

    D'cunha, J

    1997-01-01

    This article describes the second Curriculum Development Workshop held in May 1997 at the Asian Institute of Technology (AIT) in Bangkok, Thailand. The workshop aimed to review critically and restructure the Gender and Development Studies (GenDev) curriculum and to assess AIT's role in training gender experts for the region. Participants included 22 people from 16 countries in Asia, Europe, and the US who were teaching graduate students about gender issues and who were activists with nongovernmental organizations working on gender issues. It was determined that the following were required courses: Culture, Knowledge and Gender Relations; Gender, Technology, and Development; Principles of Gender Research and Methodology in Science and Technology; and Gender Analysis and Field Methods. Other suggested core courses included: Gender and Natural Resource Management; Enterprise Management, Technology, and Gender; Gender and Agrarian Reform; Urbanization: A Gender Perspective; Gender-Responsive Development Planning; and Gender and Economic Change: Past and Present Concerns. Participants distinguished between GenDev courses offered to anyone attending AIT and training courses designed to produce gender experts in the region. The aim of training courses for AIT graduate students was to sensitize potential managers, technologists, and others on gender issues and to create awareness of the importance of including gender perspectives within decision-making, policy formation, and implementation. Training courses to produce gender experts should be directed to those with a prior background in gender studies and include gender analysis in field methods. Participants agreed that there should be an independent and autonomous field of gender and development studies. Participants made six recommendations for such a field of study. PMID:12179927

  8. Skryjelites auritus gen. et sp. nov. and Quasimolites quasimodo gen. et sp. nov.-two new middle Cambrian hyolithids (?Mollusca) from the Czech Republic.

    PubMed

    Valent, Martin; Fatka, Old?ich; Szabad, Michal; Micka, Vclav; Marek, Ladislav

    2015-01-01

    Two new endemic genera and species of extinct group of Hyolitha, Skryjelites auritus gen. et sp. nov. and Quasimolites quasimodo gen. et sp. nov. are described and illustrated from the Buchava Formation of the Barrandian area (Czech Republic). PMID:26623820

  9. EPCGen2 pseudorandom number generators: analysis of J3Gen.

    PubMed

    Peinado, Alberto; Munilla, Jorge; Fster-Sabater, Amparo

    2014-01-01

    This paper analyzes the cryptographic security of J3Gen, a promising pseudo random number generator for low-cost passive Radio Frequency Identification (RFID) tags. Although J3Gen has been shown to fulfill the randomness criteria set by the EPCglobal Gen2 standard and is intended for security applications, we describe here two cryptanalytic attacks that question its security claims: (i) a probabilistic attack based on solving linear equation systems; and (ii) a deterministic attack based on the decimation of the output sequence. Numerical results, supported by simulations, show that for the specific recommended values of the configurable parameters, a low number of intercepted output bits are enough to break J3Gen. We then make some recommendations that address these issues. PMID:24721767

  10. 1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. GENERAL VIEW. Statues: Maj. Gen George Meade by Daniel Chester French, south side; Maj. Gen. John Reynolds by Charles Grafly, north side. Equestrian Statues: Maj. Gen George B. McClellan by Edward C. Potter, south side; Maj. Gen Winfield S. Hancock by J.Q.A. Ward, north side. The statue at the base of northern inner pedestal is Richard Smith, a type founder and donor of the Memorial. The niches are filled with eight colossal busts including Union generals, admirals, Pennsylvania governor, Memorial's architects (John T. and James H. Windrim), and executor of Smith's will. The frieze is carved with the names of eighty-four prominent Pennsylvania participants in the Civil War. - Smith Memorial Arch, Philadelphia, Philadelphia County, PA

  11. 98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    98. SWITCH HOUSE MAIN LOBBY, GEN 3 CIRCUIT BREAKER, VIEW OF OPPOSITE SIDE FROM HAER No. PA-505-97 - Delaware County Electric Company, Chester Station, Delaware River at South end of Ward Street, Chester, Delaware County, PA

  12. EPCGen2 Pseudorandom Number Generators: Analysis of J3Gen

    PubMed Central

    Peinado, Alberto; Munilla, Jorge; Fster-Sabater, Amparo

    2014-01-01

    This paper analyzes the cryptographic security of J3Gen, a promising pseudo random number generator for low-cost passive Radio Frequency Identification (RFID) tags. Although J3Gen has been shown to fulfill the randomness criteria set by the EPCglobal Gen2 standard and is intended for security applications, we describe here two cryptanalytic attacks that question its security claims: (i) a probabilistic attack based on solving linear equation systems; and (ii) a deterministic attack based on the decimation of the output sequence. Numerical results, supported by simulations, show that for the specific recommended values of the configurable parameters, a low number of intercepted output bits are enough to break J3Gen. We then make some recommendations that address these issues. PMID:24721767

  13. New sequestrate fungi from Guyana: Jimtrappea guyanensis gen. sp. nov., Castellanea pakaraimophila gen. sp. nov., and Costatisporus cyanescens gen. sp. nov. (Boletaceae, Boletales).

    PubMed

    Smith, Matthew E; Amses, Kevin R; Elliott, Todd F; Obase, Keisuke; Aime, M Catherine; Henkel, Terry W

    2015-12-01

    Jimtrappea guyanensis gen. sp. nov., Castellanea pakaraimophila gen. sp. nov., and Costatisporus cyanescens gen. sp. nov. are described as new to science. These sequestrate, hypogeous fungi were collected in Guyana under closed canopy tropical forests in association with ectomycorrhizal (ECM) host tree genera Dicymbe (Fabaceae subfam. Caesalpinioideae), Aldina (Fabaceae subfam. Papilionoideae), and Pakaraimaea (Dipterocarpaceae). Molecular data place these fungi in Boletaceae (Boletales, Agaricomycetes, Basidiomycota) and inform their relationships to other known epigeous and sequestrate taxa within that family. Macro- and micromorphological characters, habitat, and multi-locus DNA sequence data are provided for each new taxon. Unique morphological features and a molecular phylogenetic analysis of 185 taxa across the order Boletales justify the recognition of the three new genera. PMID:26732137

  14. SEQ-GEN: A comprehensive multimission sequencing system

    NASA Technical Reports Server (NTRS)

    Salcedo, Jose; Starbird, Thomas J.

    1994-01-01

    SEQ-GEN is a user-interactive computer program used to plan and generate a sequence of commands for spacecraft. Desired activities are specified by the user of SEQ-GEN; SEQ-GEN in turn expands these activities, deriving the spacecraft commands necessary to accomplish the desired activities. SEQ-GEN models the effects on the spacecraft of the commands, predicting the state as a function of time, flagging any conflicts and rule violations. These states, conflicts, and violations are viewable both graphically and textually at the user's request. SEQ-GEN also displays the entire sequence graphically, showing each requested activity as a bar on its graphical timeline. SEQ-GEN immediately revalidates the sequence, updating its models and calculations along with its displays based on these changes. Because it has the ability to recalculate spacecraft states immediately, the user is able to perform 'what-if' sessions easily. SEQ-GEN, a multimission tool, is adaptable to any flight project. A flight project writes its adaptation files containing project unique information including in its simplest form, only spacecraft commands. For more involved projects the adaptation files may also contain flight and mission rules, description of the spacecraft and ground models, and the definition of activities. SEQ-GEN operates at whatever level of detail the adaptation files imply. Simple adaptations are straight forward to do. There is, however, no limit to the complexity of activity definitions or of spacecraft models: both may involve unlimited logical decision points. Commands and activities may involve any number of parameters of a wide variety of data types, including integer, float, time, boolean, and character strings. SEQ-GEN will be used by the Mars Pathfinder, Cassini, and VIM (Voyager Interstellar Mission) project in an effort to speed up adaptation time and to keep sequence generation costs down. SEQ-GEN is hosted on UNIX workstations. It uses MOTIF and X for windowing, and was designed and coded in an object-oriented style in the language C++.

  15. Training trust in automation within a NextGen environment

    NASA Astrophysics Data System (ADS)

    Higham, Tiana-Lynn M.

    The projected increase in air traffic density has led to the development of NextGen that is expected to revolutionize the way the NAS is currently functioning. For NextGen to be implemented successfully, it is important to understand the humanautomation relationship within a complex system. Controllers will have to rely on automated tools to successfully manage aircraft in their sector. Increasing human trust in automation can lead to an increase in automation acceptance and its proper use. However, we are not aware of any research studies that have attempted to directly train individuals to trust automation. We report on an attempt to train 8 novice air traffic controllers to trust the automated NextGen tools in a radar internship course. Although the results were not statistically significant, the trend in the data suggests that it may be possible to train trust in automation.

  16. Enhancing Phylogeography by Improving Geographical Information from GenBank

    PubMed Central

    Scotch, Matthew; Sarkar, Indra Neil; Mei, Changjiang; Leaman, Robert; Cheung, Kei-Hoi; Ortiz, Pierina; Singraur, Ashutosh; Gonzalez, Graciela

    2011-01-01

    Phylogeography is a field that focuses on the geographical lineages of species such as vertebrates or viruses. Here, geographical data, such as location of a species or viral host is as important as the sequence information extracted from the species. Together, this information can help illustrate the migration of the species over time within a geographical area, the impact of geography over the evolutionary history, or the expected population of the species within the area. Molecular sequence data from NCBI, specifically GenBank, provide an abundance of available sequence data for phylogeography. However, geographical data is inconsistently represented and sparse across GenBank entries. This can impede analysis and in situations where the geographical information is inferred, and potentially lead to erroneous results. In this paper, we describe the current state of geographical data in GenBank, and illustrate how automated processing techniques such as named entity recognition, can enhance the geographical data available for phylogeographic studies. PMID:21723960

  17. A Virtual Reality Framework to Optimize Design, Operation and Refueling of GEN-IV Reactors.

    SciTech Connect

    Rizwan-uddin; Nick Karancevic; Stefano Markidis; Joel Dixon; Cheng Luo; Jared Reynolds

    2008-04-23

    many GEN-IV candidate designs are currently under investigation. Technical issues related to material, safety and economics are being addressed at research laboratories, industry and in academia. After safety, economic feasibility is likely to be the most important crterion in the success of GEN-IV design(s). Lessons learned from the designers and operators of GEN-II (and GEN-III) reactors must play a vital role in achieving both safety and economic feasibility goals.

  18. History of the Juliusruh ionospheric observatory on Rügen

    NASA Astrophysics Data System (ADS)

    Weiß, J.

    2016-02-01

    The history of the Juliusruh ionospheric observatory on Rügen is closely connected to the history of ground-based ionospheric sounding. After a short introduction to the ionospheric research and the sounding technique, the founding of the Juliusruh station in 1954 and its development until today are described. The different methods of ground-based sounding - as far as they apply to Juliusruh - are briefly discussed. The condition of life and work in a small team on the island of Rügen, remote from the respective parent institute, is also the subject of this article, whose author headed Juliusruh Station from 1965 to 2004.

  19. Genes and proteins of Escherichia coli (GenProtEc).

    PubMed

    Riley, M; Space, D B

    1996-01-01

    GenProtEc is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities among E.coli proteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. The database is available as a PKZip file by ftp from mbl.edu/pub/ecoli.exe. The program runs under MS-DOS on IMB-compatible machines. GenProtEc can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html. PMID:8594596

  20. 78 FR 5860 - Eighth Meeting: RTCA Next Gen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-28

    ... Federal Aviation Administration Eighth Meeting: RTCA Next Gen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA NextGen... meeting of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held February 7,...

  1. 76 FR 54526 - Fourth Meeting RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-01

    ... Federal Aviation Administration Fourth Meeting RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  2. 76 FR 22162 - Third Meeting RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-20

    ... Federal Aviation Administration Third Meeting RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  3. 77 FR 25524 - Sixth Meeting: RTCA, NextGen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-30

    ... Federal Aviation Administration Sixth Meeting: RTCA, NextGen Advisory Committee AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of a meeting of RTCA, NextGen... RTCA, NextGen Advisory Committee. DATES: The meeting will be held May 24, 2012, from 9:00 a.m.-3:00...

  4. 77 FR 54648 - Seventh Meeting: RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-05

    ... Federal Aviation Administration Seventh Meeting: RTCA NextGen Advisory Committee (NAC) AGENCY: Federal...Gen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of the seventh meeting of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held October...

  5. 78 FR 28940 - Ninth Meeting: RTCA Next Gen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-16

    ... Federal Aviation Administration Ninth Meeting: RTCA Next Gen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA NextGen... of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held June 4, 2013 from...

  6. 78 FR 54509 - Tenth Meeting: RTCA Next Gen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-04

    ... Federal Aviation Administration Tenth Meeting: RTCA Next Gen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), U.S. Department of Transportation (DOT). ACTION: Notice of RTCA NextGen... of the RTCA NextGen Advisory Committee (NAC). DATES: The meeting will be held September 19, 2013...

  7. 76 FR 3931 - Second Meeting RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-21

    ... Federal Aviation Administration Second Meeting RTCA NextGen Advisory Committee (NAC) AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: RTCA NextGen Advisory Committee (NAC). SUMMARY: The FAA is issuing this notice to advise the public of a meeting of RTCA NextGen Advisory Committee (NAC). DATES:...

  8. GenAnneal: Genetically modified Simulated Annealing

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, Isaac E.

    2006-05-01

    A modification of the standard Simulated Annealing (SA) algorithm is presented for finding the global minimum of a continuous multidimensional, multimodal function. We report results of computational experiments with a set of test functions and we compare to methods of similar structure. The accompanying software accepts objective functions coded both in Fortran 77 and C++. Program summaryTitle of program:GenAnneal Catalogue identifier:ADXI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXI_v1_0 Program available from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The tool is designed to be portable in all systems running the GNU C++ compiler Installation: University of Ioannina, Greece on Linux based machines Programming language used:GNU-C++, GNU-C, GNU Fortran 77 Memory required to execute with typical data: 200 KB No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: No No. of bytes in distributed program, including test data, etc.:84 885 No. of lines in distributed program, including test data, etc.:14 896 Distribution format: tar.gz Nature of physical problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a non-linear system of equations via optimization, employing a "least squares" type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero). Typical running time: Depending on the objective function. Method of solution: We modified the process of step selection that the traditional Simulated Annealing employs and instead we used a global technique based on grammatical evolution.

  9. DOE/NNSA perspective safeguard by design: GEN III/III+ light water reactors and beyond

    SciTech Connect

    Pan, Paul Y

    2010-12-10

    An overview of key issues relevant to safeguards by design (SBD) for GEN III/IV nuclear reactors is provided. Lessons learned from construction of typical GEN III+ water reactors with respect to SBD are highlighted. Details of SBD for safeguards guidance development for GEN III/III+ light water reactors are developed and reported. This paper also identifies technical challenges to extend SBD including proliferation resistance methodologies to other GEN III/III+ reactors (except HWRs) and GEN IV reactors because of their immaturity in designs.

  10. Meet Mr. and Mrs. Gen X: A New Parent Generation

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. In the early 1990s, Gen Xers began joining parent-teacher associations in the nation's elementary schools. Around 2005, they became the majority of middle school parents. By the fall of 2008, they took over

  11. Boomers, Gen-Xers, and Millennials: Understanding the "New Students."

    ERIC Educational Resources Information Center

    Oblinger, Diana

    2003-01-01

    Describes characteristics of the "new" college student, who may be an adult learner from the Baby Boomer era, a high school member of the "Millennial" generation, or a "Gen-Xer." Explores the learning styles of each type of student and discusses the importance of technology to each group. (SLD)

  12. Safer Systems: A NextGen Aviation Safety Strategic Goal

    NASA Technical Reports Server (NTRS)

    Darr, Stephen T.; Ricks, Wendell R.; Lemos, Katherine A.

    2008-01-01

    The Joint Planning and Development Office (JPDO), is charged by Congress with developing the concepts and plans for the Next Generation Air Transportation System (NextGen). The National Aviation Safety Strategic Plan (NASSP), developed by the Safety Working Group of the JPDO, focuses on establishing the goals, objectives, and strategies needed to realize the safety objectives of the NextGen Integrated Plan. The three goal areas of the NASSP are Safer Practices, Safer Systems, and Safer Worldwide. Safer Practices emphasizes an integrated, systematic approach to safety risk management through implementation of formalized Safety Management Systems (SMS) that incorporate safety data analysis processes, and the enhancement of methods for ensuring safety is an inherent characteristic of NextGen. Safer Systems emphasizes implementation of safety-enhancing technologies, which will improve safety for human-centered interfaces and enhance the safety of airborne and ground-based systems. Safer Worldwide encourages coordinating the adoption of the safer practices and safer systems technologies, policies and procedures worldwide, such that the maximum level of safety is achieved across air transportation system boundaries. This paper introduces the NASSP and its development, and focuses on the Safer Systems elements of the NASSP, which incorporates three objectives for NextGen systems: 1) provide risk reducing system interfaces, 2) provide safety enhancements for airborne systems, and 3) provide safety enhancements for ground-based systems. The goal of this paper is to expose avionics and air traffic management system developers to NASSP objectives and Safer Systems strategies.

  13. AnoGen: A Program for Generating ANOVA Data Sets.

    ERIC Educational Resources Information Center

    Miller, Jeff

    1999-01-01

    Describes a computer program called AnoGen that automates the process of generating data sets for ANOVA designs and operates within DOS and Windows compatible computers. Explains that the program runs in both student and teacher modes and is freely available for noncommercial use through the Internet. (CMK)

  14. Biogas Purification Process to Increase GenSet Efficiency

    NASA Astrophysics Data System (ADS)

    Krido Wahono, Satriyo; Maryana, Roni; Kismurtono, M.

    2009-09-01

    Because of global issue about limited energy, biogas was one of alternative energy and save energy in the world which produced from biomass especially from cow manure. Most of biogas which produced from cow manure contains 40-75% methane as energy resources and another gas as impurities. Methane concentration of biogas has relation with biogas energy value, especially for application as fuel of electricity conversion using gen-set. For increasing gen-set efficiency can be held by increasing methane concentration of biogas using biogas purification process. Biogas purification process can be held by adsorption system which using activated zeolite as absorber. After biogas through the purification system, methane concentration was increasing and impacting to gen-set efficiency especially voltage value was increasing until 22 times in average better than without purification and keeping power stability, so it will produce electricity conversion until 39,07% of practical and 38,09% of equation calculation from maximum electric power output of gen-set.

  15. A New Parent Generation: Meet Mr. and Mrs. Gen X

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. Gen-X parents and Boomer parents belong to two neighboring generations, each possessing its own location in history and its own peer personality. They are similar in some respects, but clearly different in

  16. Fossil energy, clean coal technology, and FutureGen

    SciTech Connect

    Sarkus, T.A.

    2008-07-15

    Future fossil use will rely heavily on carbon sequestration. Clean coal technologies are being incorporated in the USA, including air pollution control, and will need to incorporate carbon capture and sequestration. The paper ends with an outline of the restructured FutureGen project. 7 figs.

  17. Meet Mr. and Mrs. Gen X: A New Parent Generation

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. In the early 1990s, Gen Xers began joining parent-teacher associations in the nation's elementary schools. Around 2005, they became the majority of middle school parents. By the fall of 2008, they took over…

  18. 75 FR 56654 - RTCA NextGen Advisory Committee (NAC)

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-16

    ... Notice in the Federal Register on September 3, 2010 (75-FR-54221), concerning a Notice to advise the... the Federal Register Notice on September 3, 2010, (75-FR-54221) is revised to read as follows: Opening... Federal Aviation Administration RTCA NextGen Advisory Committee (NAC) AGENCY: Federal...

  19. A New Parent Generation: Meet Mr. and Mrs. Gen X

    ERIC Educational Resources Information Center

    Howe, Neil

    2010-01-01

    Slowly but surely, Generation Xers have been taking over from Baby Boomers as the majority of parents in elementary and secondary education. Gen-X parents and Boomer parents belong to two neighboring generations, each possessing its own location in history and its own peer personality. They are similar in some respects, but clearly different in…

  20. An electronic flight bag for NextGen avionics

    NASA Astrophysics Data System (ADS)

    Zelazo, D. Eyton

    2012-06-01

    The introduction of the Next Generation Air Transportation System (NextGen) initiative by the Federal Aviation Administration (FAA) will impose new requirements for cockpit avionics. A similar program is also taking place in Europe by the European Organisation for the Safety of Air Navigation (Eurocontrol) called the Single European Sky Air Traffic Management Research (SESAR) initiative. NextGen will require aircraft to utilize Automatic Dependent Surveillance-Broadcast (ADS-B) in/out technology, requiring substantial changes to existing cockpit display systems. There are two ways that aircraft operators can upgrade their aircraft in order to utilize ADS-B technology. The first is to replace existing primary flight displays with new displays that are ADS-B compatible. The second, less costly approach is to install an advanced Class 3 Electronic Flight Bag (EFB) system. The installation of Class 3 EFBs in the cockpit will allow aircraft operators to utilize ADS-B technology in a lesser amount of time with a decreased cost of implementation and will provide additional benefits to the operator. This paper describes a Class 3 EFB, the NexisTM Flight-Intelligence System, which has been designed to allow users a direct interface with NextGen avionics sensors while additionally providing the pilot with all the necessary information to meet NextGen requirements.

  1. EnGenIUS -- Environmental Genome Informational Utility System.

    PubMed

    Kaplarevic, Mihailo; Murray, Alison E; Cary, Stephen C; Gao, Guang R

    2008-12-01

    Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as single reads. Most existing annotation systems and genome databases accommodate assembled genomes containing contiguous gene-encoding sequences. Thus, a solution is required that can work effectively with environmental genomic annotation information to facilitate data analysis. The Environmental Genome Informational Utility System (EnGenIUS) is a comprehensive environmental genome (metagenome) research toolset that was specifically designed to accommodate the needs of large (> 250 K sequence reads) environmental genome sequencing efforts. The core EnGenIUS modules consist of a set of UNIX scripts and PHP programs used for data preprocessing, an annotation pipeline with accompanying analysis tools, two entity relational databases, and a graphical user interface. The annotation pipeline has a modular structure and can be customized to best fit input data set properties. The integrated entity relational databases store raw data and annotation analysis results. Access to the underlying databases and services is facilitated through a web-based graphical user interface. Users have the ability to browse, upload, download, and analyze preprocessed data, based on diverse search criteria. The EnGenIUS toolset was successfully tested using the Alvinella pompejana epibiont environmental genome data set, which comprises more than 300 K sequence reads. A fully browsable EnGenIUS portal is available at (http://ocean.dbi.udel.edu/) (access code: "guest"). The scope of this paper covers the implementation details and technical aspects of the EnGenIUS toolset. PMID:19090024

  2. Advanced Vehicle Concepts and Implications for NextGen

    NASA Technical Reports Server (NTRS)

    Blake, Matt; Smith, Jim; Wright, Ken; Mediavilla Ricky; Kirby, Michelle; Pfaender, Holger; Clarke, John-Paul; Volovoi, Vitali; Dorbian, Christopher; Ashok, Akshay; Reynolds, Tom; Waitz, Ian; Hileman, James; Arunachalam, Sarav; Hedrick, Matt; Vempati, Lakshmi; Laroza, Ryan; denBraven, Wim; Henderson, Jeff

    2010-01-01

    This report presents the results of a major NASA study of advanced vehicle concepts and their implications for the Next Generation Air Transportation System (NextGen). Comprising the efforts of dozens of researchers at multiple institutions, the analyses presented here cover a broad range of topics including business-case development, vehicle design, avionics, procedure design, delay, safety, environmental impacts, and metrics. The study focuses on the following five new vehicle types: Cruise-efficient short takeoff and landing (CESTOL) vehicles Large commercial tiltrotor aircraft (LCTRs) Unmanned aircraft systems (UAS) Very light jets (VLJs) Supersonic transports (SST). The timeframe of the study spans the years 2025-2040, although some analyses are also presented for a 3X scenario that has roughly three times the number of flights as today. Full implementation of NextGen is assumed.

  3. Coal-Gen attendees hear there's no magic bullet

    SciTech Connect

    2007-09-15

    Those attending COAL-GEN 2007 in August heard that there is no magic bullet for meeting the energy and infrastructure needs facing the USA. The article reports on the conference which addressed topics including development of supercritical circulating fluidized bed coal unit; IGCC projects, the importance of including carbon capture and sequestration, and the need to attract and train personnel to work in the power industry. 3 photos.

  4. PowerGen Plc -- A commercial user of Orimulsion

    SciTech Connect

    Tombs, R.; Jones, A.

    1996-12-31

    PowerGen has been operating two power stations commercially on Orimulsion fuel since 1991. Prior to the conversions, both power stations, Ince and Richborough, experienced low load factors caused by the inconsistent, but on average, high fuel oil prices. Orimulsion provided an opportunity of economic operation at both power stations if it could be proved that the fuel could be burnt safely, efficiently and cleanly. Consequently, a series of trials was organized at both plants and these commenced in 1988. Ince was the first plant to use Orimulsion when single burner trials were conducted with the objective of selecting a suitable burner system for subsequent full boiler trials. Having developed burners which would ensure stable and clean combustion, full scale boiler trials were undertaken at both power stations in 1989. The key objectives of these trials were to establish the impact on the plant of handling and burning the fuel, to define hardware modifications that would be required for commercial operation and for the operators to gain experience with Orimulsion. Following different levels of plant modification at Ince and Richborough Power Stations, judged necessary as a result of the trials, commercial operation was begun. Since late 1991, PowerGen has consumed about 1.3m tonnes of Orimulsion each year. PowerGen has been able to develop a unique knowledge on all aspects of handling and burning Orimulsion. The intent of this paper is to provide an update of their experience under commercial operation.

  5. GEN IV reactors: Where we are, where we should go

    SciTech Connect

    Locatelli, G.; Mancini, M.; Todeschini, N.

    2012-07-01

    GEN IV power plants represent the mid-long term option of the nuclear sector. International literature proposes many papers and reports dealing with these reactors, but there is an evident difference of type and shape of information making impossible each kind of detailed comparison. Moreover, authors are often strongly involved in some particular design; this creates many difficulties in their super-partes position. Therefore it is necessary to put order in the most relevant information to understand strengths and weaknesses of each design and derive an overview useful for technicians and policy makers. This paper presents the state-of the art for GEN IV nuclear reactors providing a comprehensive literature review of the different designs with a relate taxonomy. It presents the more relevant references, data, advantages, disadvantages and barriers to the adoptions. In order to promote an efficient and wide adoption of GEN IV reactors the paper provides the pre-conditions that must be accomplished, enabling factors promoting the implementation and barriers limiting the extent and intensity of its implementation. It concludes outlying the state of the art of the most important R and D areas and the future achievements that must be accomplished for a wide adoption of these technologies. (authors)

  6. Recent changes in the GenBank On-line Service.

    PubMed

    Benton, D

    1990-03-25

    The GenBank On-line Service provides access to the GenBank and EMBL nucleic acid sequence databases and to the Swiss-Prot and GenPept protein sequence databases. Users can query the databases by sequence similarity and annotation keywords and retrieve entries of interest. This access is available through e-mail servers, anonymous FTP, anonymous interactive login, and login to established, password-protected, individual accounts. PMID:2326192

  7. Remarks on Peinado et al.'s Analysis of J3Gen

    PubMed Central

    Garcia-Alfaro, Joaquin; Herrera-Joancomart, Jordi; Meli-Segu, Joan

    2015-01-01

    Peinado et al. analyzed the security of the J3Gen pseudorandom number generator proposed by Meli-Segu et al., and claimed weaknesses regarding its security properties. They also presented a deterministic attack based on the decimation of the J3Gen output sequences. We show that the assumptions made by Peinado et al. are not correct and that the proposed deterministic attack against J3Gen does not hold in practice. PMID:25781510

  8. Remarks on Peinado et al.'s Analysis of J3Gen.

    PubMed

    Garcia-Alfaro, Joaquin; Herrera-Joancomartí, Jordi; Melià-Seguí, Joan

    2015-01-01

    Peinado et al. analyzed the security of the J3Gen pseudorandom number generator proposed by Melià-Seguí et al., and claimed weaknesses regarding its security properties. They also presented a deterministic attack based on the decimation of the J3Gen output sequences. We show that the assumptions made by Peinado et al. are not correct and that the proposed deterministic attack against J3Gen does not hold in practice. PMID:25781510

  9. Pantanalinema gen. nov. and Alkalinema gen. nov.: novel pseudanabaenacean genera (Cyanobacteria) isolated from saline-alkaline lakes.

    PubMed

    Vieira Vaz, Marcelo Gomes Maral; Genurio, Diego Bonaldo; Andreote, Ana Paula Dini; Malone, Camila Francieli Silva; Sant'Anna, Clia Leite; Barbiero, Laurent; Fiore, Marli Ftima

    2015-01-01

    The genus Leptolyngbya Anagnostidis & Komrek (1988) was described from a set of strains identified as 'LPP-group B'. The morphology within this group is not particularly informative and underestimates the group's genetic diversity. In the present study, two new pseudanabaenacean genera related to Leptolyngbya morphotypes, Pantanalinema gen. nov. and Alkalinema gen. nov., are described under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants, based on a polyphasic approach. Pantanalinema gen. nov. (type species Pantanalinema rosaneae sp. nov.) has sheaths and trichomes with slight gliding motility, which distinguish this genus from Alkalinema gen. nov. (type species Alkalinema pantanalense sp. nov.), which possesses trichomes arranged in an ornate (interwoven) pattern. 16S rRNA gene sequences of strains of Pantanalinema and Alkalinema exhibited low identity to each other (?91.6?%) and to other sequences from known pseudanabaenacean genera (?94.3 and 93.7?%, respectively). In a phylogenetic reconstruction, six sequences from strains of Pantanalinema and four from strains of Alkalinema formed two separate and robust clades (99?% bootstrap value), with the genera Oculatella and Phormidesmis, respectively, as the closest related groups. 16S-23S rRNA intergenic spacer sequences and secondary structures of strains of Pantanalinema and Alkalinema did not correspond to any previous descriptions. The strains of Pantanalinema and Alkalinema were able to survive and produce biomass at a range of pH (pH 4-11) and were also able to alter the culture medium to pH values ranging from pH 8.4 to 9.9. These data indicate that cyanobacterial communities in underexplored environments, such as the Pantanal wetlands, are promising sources of novel taxa. PMID:25351877

  10. GRAIL and GenQuest Sequence Annotation Tools

    SciTech Connect

    Xu, Ying; Shah, Manesh B.; Einstein, J. Ralph; Parang, Morey; Snoddy, Jay; Petrov, Sergey; Olman, Victor; Zhang, Ge; Mural, Richard J.; Uberbacher, Edward C.

    1997-12-31

    Our goal is to develop and implement an integrated intelligent system which can recognize biologically significant features in DNA sequence and provide insight into the organization and function of regions of genomic DNA. GRAIL is a modular expert system which facilitates the recognition of gene features and provides an environment for the construction of sequence annotation. The last several years have seen a rapid evolution of the technology for analyzing genomic DNA sequences. The current GRAIL systems (including the e-mail, XGRAIL, JAVA-GRAIL and genQuest systems) are perhaps the most widely used, comprehensive, and user friendly systems available for computational characterization of genomic DNA sequence.

  11. Frigitilla gen. nov., a new genus of Amazonian Mutillidae (Hymenoptera).

    PubMed

    Bartholomay, Pedro R; Williams, Kevin A; Luz, David R; Morato, Elder F

    2015-01-01

    Mutilla frigidula Cresson, 1902 was transferred to Tobantilla by Williams et al. (2011), based on morphological similarities with females of that genus. Discovery of the male of this species indicated significant morphological differences from Tobantilla. We therefore erect the genus, Frigitilla gen. nov., for Mutilla frigidula. Herein, we describe the male of F. frigidula (Cresson, 1902), comb. nov., associate it with its host (Trypoxylon spp.), and discuss its relations to other mutillid genera. The impact of collecting method and specimen age on the integumental coloration of specimens is discussed, emphasizing the need to diagnose species on consistent structural features rather than differences in color pattern. PMID:26249052

  12. Meloneis Gen. Nov., a New Epipsammic Genus of Rhaphoneidaceae (Bacillariophyceae)

    PubMed Central

    Louvrou, Ioanna; Danielidis, Daniel B.; Economou-Amilli, Athena

    2012-01-01

    The diatom family Rhaphoneidaceae is characterized by high generic diversity and low species diversity with most genera known to have long stratigraphic ranges. The genera within this family are neritic marine, and mostly epipsammic. A new modern and epipsammic genus, Meloneis gen. nov., is described herein and is compared to all genera within Rhaphoneidaceae and especially to Rhaphoneis Ehrenberg s.l. Within Meloneis three new species and one variety are distinguished and described herein: M. mimallis sp. nov., M. mimallis var. zephyria var. nov., M. akytos sp. nov., and M. gorgis sp. nov. PMID:22442663

  13. The GenBank nucleic acid sequence database.

    PubMed

    Burks, C; Fickett, J W; Goad, W B; Kanehisa, M; Lewitter, F I; Rindone, W P; Swindell, C D; Tung, C S; Bilofsky, H S

    1985-12-01

    The GenBank nucleic acid sequence database is a computer-based collection of all published DNA and RNA sequences; it contains over five million bases in close to six thousand sequence entries drawn from four thousand five hundred published articles. Each sequence is accompanied by relevant biological annotation. The database is available either on magnetic tape, on floppy diskettes, on-line or in hardcopy form. We discuss the structure of the database, the extent of the data and the implications of the database for research on nucleic acids. PMID:3880345

  14. Power-Gen Americas: Small gas turbines are big news

    SciTech Connect

    1996-01-01

    The era of the small gas turbine-generator may be nearly upon us. At Power-Gen Americas `95 in Anaheim, California (near Los Angeles), no less than three manufacturers, Allied Signal Aerospace, Capstone Turbine and Elliot Energy Systems, displayed prototype units with outputs in the 20-50 MW class. Perhaps coincidentally, all had a single-stage centrifugal compressor and single-stage radial-inflow turbine, mounted on a common shaft with the generator/alternator. And all had, or will have, a recuperator. This paper briefly describes the specifications and applications of the systems presented. 4 figs.

  15. VitisGen on the road: mapping the way to the next generation of grapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-NIFA VitisGen project (Award No. 2011-51181-30635) aims to optimize grape cultivar improvement through the integration of grape breeding, cutting edge genomics technology, precision phenotyping, socioeconomic research, and extension. VitisGen is a five-year project involving 25 co-PIs at 11...

  16. CottonGen: a genomics, genetics and breeding database for cotton research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

  17. 76 FR 15039 - RTCA Government/Industry NextGen Advisory Committee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION Federal Aviation Administration RTCA Government/Industry NextGen Advisory Committee AGENCY: Federal...-9434; Web site http://www.rtca.org or the FAA Business Operations Group, NextGen and...

  18. Spatial control of the GEN1 Holliday junction resolvase ensures genome stability

    PubMed Central

    Chan, Ying Wai; West, Stephen C.

    2014-01-01

    Holliday junction (HJ) resolvases are necessary for the processing of persistent recombination intermediates before cell division. Their actions, however, need to be restricted to the late stages of the cell cycle to avoid the inappropriate cleavage of replication intermediates. Control of the yeast HJ resolvase, Yen1, involves phosphorylation changes that modulate its catalytic activity and nuclear import. Here, we show that GEN1, the human ortholog of Yen1, is regulated by a different mechanism that is independent of phosphorylation. GEN1 is controlled exclusively by nuclear exclusion, driven by a nuclear export signal (NES) that restricts GEN1 actions to mitosis when the nuclear membrane breaks down. Construction of a nuclear-localized version of GEN1 revealed that its premature actions partially suppress phenotypes associated with loss of BLM and MUS81, but cause elevated crossover formation. The spatial control of GEN1 therefore contributes to genome stability, by avoiding competition with non-crossover promoting repair pathways. PMID:25209024

  19. Spatial control of the GEN1 Holliday junction resolvase ensures genome stability.

    PubMed

    Chan, Ying Wai; West, Stephen C

    2014-01-01

    Holliday junction (HJ) resolvases are necessary for the processing of persistent recombination intermediates before cell division. Their actions, however, need to be restricted to the late stages of the cell cycle to avoid the inappropriate cleavage of replication intermediates. Control of the yeast HJ resolvase, Yen1, involves phosphorylation changes that modulate its catalytic activity and nuclear import. Here, we show that GEN1, the human ortholog of Yen1, is regulated by a different mechanism that is independent of phosphorylation. GEN1 is controlled exclusively by nuclear exclusion, driven by a nuclear export signal (NES) that restricts GEN1 actions to mitosis when the nuclear membrane breaks down. Construction of a nuclear-localized version of GEN1 revealed that its premature actions partially suppress phenotypes associated with loss of BLM and MUS81, but cause elevated crossover formation. The spatial control of GEN1 therefore contributes to genome stability, by avoiding competition with non-crossover promoting repair pathways. PMID:25209024

  20. 77 FR 52352 - Notice of Intent To Prepare an Environmental Impact Statement for the Rio Mesa Gen-Tie Project...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-29

    ... Gen-Tie Project and Possible Land Use Plan Amendment, Riverside County, CA AGENCY: Bureau of Land..., California, intends to prepare an Environmental Impact Statement (EIS) for the Rio Mesa Gen- Tie Project. The... Gen-Tie Project by any of the following methods: Web site: http://www.blm.gov/ca/st/en.html ;...

  1. Hunting for new restriction enzymes in GenBank

    SciTech Connect

    Roberts, R.J.

    1997-12-01

    Restriction enzyme genes are hard to identify unless their surrounding sequences are available. This is because the best definition of a restriction enzyme gene is an open reading frame, that looks like nothing else in GenBank, but lies close to a DNA methylase gene. There are other clues too, such as nearby reading frames that code control proteins or the DNA specificity subunits of Type I restriction enzymes. We are developing software that searches the daily updates of GenBank to find candidate restriction enzyme genes. This is being followed by bench experiments to see of the predictions are correct. More than 50 potential new restriction enzymes have been predicted and it is quite remarkable that the density of restriction enzyme genes in microbial DNA is greater than one system per 200 Kb. The software development is emphasizing the graphic presentation of the search results. The approach could be used for other situations where a molecular biologist is interested to find new examples of their favorite genes.

  2. Nuclear Data Needs for the Assessment of Gen IV Systems

    NASA Astrophysics Data System (ADS)

    Rimpault, Gerald

    2006-04-01

    Four of the six nuclear systems identified by the Gen-IV international forum are relying in fast reactors. The high performance required from these future FR's calls for very innovative core characteristics compared with conventional fast reactor designs, which in turns give rise to new challenges for the available neutronics methods and data. The ERANOS formulaire was developed for reliable, precise and efficient calculations of sodium-cooled fast neutron reactor cores. Such a formulaire enables the prediction of all the neutronic quantities of interest for reactor design, operation and safety studies, along with their corresponding uncertainties. Given its achievement in terms of accuracy for existing sodium cooled reactors, the way the ERANOS formulaire has been designed should be looked as an example for developing similar tools for GENIV fast cores. The methodology for defining nuclear data needs is briefly covered. Target accuracies for GEN-IV neutronic characteristics is an important point to start with. The covariance data is of significant importance for quantifying the needs and evaluators should provide them with their nuclear data. Hence, nuclear data requests should be associated to uncertainty values. Integral experiments have a complementary role to differential measurements for meeting some nuclear data needs (for instance Pu239 fission). High Priority Level Requests should include those nuclides accessible with current differential measurement technology and should include less important nuclides A list of potential requests is existing, quantifying their uncertainties remain a significant effort particularly when looking at fuel cycle quantities.

  3. Mutation and association analysis of GEN1 in breast cancer susceptibility

    PubMed Central

    Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Evans, D. Gareth; Eccles, Diana; Stratton, Michael R.

    2013-01-01

    GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519del-AAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale casecontrol association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

  4. Mutation and association analysis of GEN1 in breast cancer susceptibility.

    PubMed

    Turnbull, Clare; Hines, Sarah; Renwick, Anthony; Hughes, Deborah; Pernet, David; Elliott, Anna; Seal, Sheila; Warren-Perry, Margaret; Gareth Evans, D; Eccles, Diana; Stratton, Michael R; Rahman, Nazneen

    2010-11-01

    GEN1 was recently identified as a key Holliday junction resolvase involved in homologous recombination. Somatic truncating GEN1 mutations have been reported in two breast cancers. Together these data led to the proposition that GEN1 is a breast cancer predisposition gene. In this article we have formally investigated this hypothesis. We performed full-gene mutational analysis of GEN1 in 176 BRCA1/2-negative familial breast cancer samples and 159 controls. We genotyped six SNPs tagging the 30 common variants in the transcribed region of GEN1 in 3,750 breast cancer cases and 4,907 controls. Mutation analysis revealed one truncating variant, c.2515_2519delAAGTT, which was present in 4% of cases and 4% of controls. We identified control individuals homozygous for the deletion, demonstrating that the last 69 amino acids of GEN1 are dispensable for its function. We identified 17 other variants, but their frequency did not significantly differ between cases and controls. Analysis of 3,750 breast cancer cases and 4,907 controls demonstrated no evidence of significant association with breast cancer for six SNPs tagging the 30 common GEN1 variants. These data indicate that although it also plays a key role in double-strand DNA break repair, GEN1 does not make an appreciable contribution to breast cancer susceptibility by acting as a high- or intermediate-penetrance breast cancer predisposition gene like BRCA1, BRCA2, CHEK2, ATM, BRIP1 and PALB2 and that common GEN1 variants do not act as low-penetrance susceptibility alleles analogous to SNPs in FGFR2. Furthermore, our analyses demonstrate the importance of undertaking appropriate genetic investigations, typically full gene screening in cases and controls together with large-scale case-control association analyses, to evaluate the contribution of genes to cancer susceptibility. PMID:20512659

  5. New Boletaceae taxa from Guyana: Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov., Singerocomus rubriflavus gen. and sp. nov., and a new combination for Xerocomus inundabilis.

    PubMed

    Henkel, Terry W; Obase, Keisuke; Husbands, Dillon; Uehling, Jessie K; Bonito, Gregory; Aime, M Catherine; Smith, Matthew E

    2016-01-01

    Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov. and Singerocomus rubriflavus gen. and sp. nov. (Boletaceae, Boletales, Basidiomycota) are described from the Pakaraima Mountains and adjacent lowlands of Guyana. Xerocomus inundabilis, originally described from the central Brazilian Amazon and based solely on the type collection, is redescribed from numerous collections from Guyana and transferred into Singerocomus. These boletes occur in Neotropical forests dominated by ectomycorrhizal trees in the genera Dicymbe (Fabaceae subfam. Caesalpinioideae), Aldina (Fabaceae subfam. Papilionoideae) and Pakaraimaea (Dipterocarpaceae). Three of the species were repeatedly found in a multiyear sporocarp survey in Dicymbe corymbosa-monodominant forest. Macromorphological, micromorphological, habitat and multilocus DNA sequence data are provided for each species. A molecular phylogenetic analysis based on a large taxon set across the Boletaceae justifies erection of the new genera. PMID:26490700

  6. Decay heat removal in GEN IV gas cooled fast reactors.

    SciTech Connect

    Cheng, L. Y.; Wei, T. Y. C.

    2009-08-01

    The safety goal of the current designs of advanced high-temperature thermal gas-cooled reactors (HTRs) is that no core meltdown would occur in a depressurization event with a combination of concurrent safety system failures. This study focused on the analysis of passive decay heat removal (DHR) in a GEN IV direct-cycle gas-cooled fast reactor (GFR) which is based on the technology developments of the HTRs. Given the different criteria and design characteristics of the GFR, an approach different from that taken for the HTRs for passive DHR would have to be explored. Different design options based on maintaining core flow were evaluated by performing transient analysis of a depressurization accident using the system code RELAP5-3D. The study also reviewed the conceptual design of autonomous systems for shutdown decay heat removal and recommends that future work in this area should be focused on the potential for Brayton cycle DHRs.

  7. What Can a Historian Do with AstroGen?

    NASA Astrophysics Data System (ADS)

    Tenn, Joseph S.

    2015-01-01

    "Astrogen", the Astronomy Genealogy Project, is in the development stage. Patterned after the Mathematics Genealogy Project at http://genealogy.math.ndsu.nodak.edu, it will eventually include most of the world's astronomers, past and present, and provide information about their years of life, highest degrees, universities, and thesis titles. There will also be links to online theses, home pages, and obituaries when these are available. Although a few details remain to be worked out before it becomes public, it is possible to make some use of what has already been compiled. I will give an example, comparing graduates of Harvard University, the University of California at Berkeley, and the University of Chicago from different decades, with information about their professional careers and publication records. The author welcomes queries about AstroGen and is seeking more participants.

  8. PopGen: A virtual human population generator.

    PubMed

    McNally, Kevin; Cotton, Richard; Hogg, Alex; Loizou, George

    2014-01-01

    The risk assessment of environmental chemicals and drugs is moving towards a paradigm shift in approach which seeks the full replacement animal testing with high throughput, mechanistic, in vitro systems. This new vision will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated using in vitro, in silico and in chemico systems, can be integrated and utilised for quantitative in vitro-to-in vivo extrapolation (QIVIVE), ultimately to the human population level. Physiologically based pharmacokinetic (PBPK) models are ideally suited for this and are obligatory in order to translate in vitro concentration-response relationships to an exposure or dose, route and duration regime in people. In this report we describe PopGen, a virtual human population generator which is a user friendly, open access web-based application for the prediction of realistic anatomical, physiological and phase 1 metabolic variation in a wide range of healthy human populations. We demonstrate how PopGen can be used for QIVIVE by providing input to a PBPK model, at an appropriate level of detail, to reconstruct exposure from human biomonitoring data. We discuss how the process of exposure reconstruction from blood biomarkers, in general, is analogous to exposure or dose reconstruction from concentration-response measurements made in proposed in vitro cell based systems which are assumed to be surrogates for target organs. PMID:23876857

  9. Reprint of PopGen: A virtual human population generator.

    PubMed

    McNally, Kevin; Cotton, Richard; Hogg, Alex; Loizou, George

    2015-06-01

    The risk assessment of environmental chemicals and drugs is moving towards a paradigm shift in approach which seeks the full replacement animal testing with high throughput, mechanistic, in vitro systems. This new vision will be reliant on the measurement in vitro, of concentration-dependent responses where prolonged excessive perturbations of specific biochemical pathways are likely to lead to adverse health effects in an intact organism. Such an approach requires a framework, into which disparate data generated using in vitro, in silico and in chemico systems, can be integrated and utilised for quantitative in vitro-to-in vivo extrapolation (QIVIVE), ultimately to the human population level. Physiologically based pharmacokinetic (PBPK) models are ideally suited for this and are obligatory in order to translate in vitro concentration-response relationships to an exposure or dose, route and duration regime in people. In this report we describe PopGen a virtual human population generator which is a user friendly, open access web-based application for the prediction of realistic anatomical, physiological and phase 1 metabolic variation in a wide range of healthy human populations. We demonstrate how PopGen can be used for QIVIVE by providing input to a PBPK model, at an appropriate level of detail, to reconstruct exposure from human biomonitoring data. We discuss how the process of exposure reconstruction from blood biomarkers, in general, is analogous to exposure or dose reconstruction from concentration-response measurements made in proposed in vitro cell based systems which are assumed to be surrogates for target organs. PMID:25921244

  10. Use of experimental design to optimize docking performance: the case of LiGenDock, the docking module of LiGen, a new de novo design program.

    PubMed

    Beato, Claudia; Beccari, Andrea R; Cavazzoni, Carlo; Lorenzi, Simone; Costantino, Gabriele

    2013-06-24

    On route toward a novel de novo design program, called LiGen, we developed a docking program, LiGenDock, based on pharmacophore models of binding sites, including a non-enumerative docking algorithm. In this paper, we present the functionalities of LiGenDock and its accompanying module LiGenPocket, aimed at the binding site analysis and structure-based pharmacophore definition. We also report the optimization procedure we have carried out to improve the cognate docking and virtual screening performance of LiGenDock. In particular, we applied the design of experiments (DoE) methodology to screen the set of user-adjustable parameters to identify those having the largest influence on the accuracy of the results (which ensure the best performance in pose prediction and in virtual screening approaches) and then to choose their optimal values. The results are also compared with those obtained by two popular docking programs, namely, Glide and AutoDock for pose prediction, and Glide and DOCK6 for Virtual Screening. PMID:23590204

  11. Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria.

    PubMed

    Johnson, D Barrie; Bacelar-Nicolau, Paula; Okibe, Naoko; Thomas, Angharad; Hallberg, Kevin B

    2009-05-01

    Two novel extremely acidophilic, iron-oxidizing actinobacteria were isolated, one from a mine site in North Wales, UK (isolate T23(T)), and the other from a geothermal site in Yellowstone National Park, Wyoming, USA (Y005(T)). These new actinobacteria belong to the subclass Acidimicrobidae, and in contrast to the only other classified member of the subclass (Acidimicrobium ferrooxidans), both isolates were obligate heterotrophs. The mine site isolate was mesophilic and grew as small rods, while the Yellowstone isolate was a moderate thermophile and grew as long filaments, forming macroscopic flocs in liquid media. Both isolates accelerated the oxidative dissolution of pyrite in yeast extract-amended cultures, but neither was able to oxidize reduced forms of sulfur. Ferrous iron oxidation enhanced growth yields of the novel mesophilic actinobacterium T23(T), though this was not confirmed for the Yellowstone isolate. Both isolates catalysed the dissimilatory reduction of ferric iron, using glycerol as electron donor, in oxygen-free medium. Based on comparative analyses of base compositions of their chromosomal DNA and of their 16S rRNA gene sequences, the isolates are both distinct from each other and from Acidimicrobium ferrooxidans, and are representatives of two novel genera. The names Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov. are proposed for the mesophilic and moderately thermophilic isolates, respectively, with the respective type strains T23(T) (=DSM 19497(T)=ATCC BAA-1647(T)) and Y005(T) (=DSM 19514(T)=ATCC BAA-1645(T)). PMID:19406797

  12. Experiment study on compatibility between high performance microchannel plate and gen III image intensifier

    NASA Astrophysics Data System (ADS)

    Liu, Shulin; Zhu, Yufeng; Shi, Feng; Nie, Jing; Zhang, Taimin; Liu, Xiaojian; Zhang, Ni; Liu, Zhaolu; He, Yingping; Bai, Xiaofeng; Sun, Jiannin; Pan, Jinsheng; Cong, Xiaoqing

    2011-08-01

    To make sure that high performance Microchannel Plate (HP-MCP) can be applied successfully in Gen III Image Intensifier, vacuum baking test and trying out test are carried out first, then making ion barrier film onto input surface of HP-MCP, employing strict electron scrubbing test, and measuring resistance, gain in each stage, finally Gen III Image intensifier is manufactured with HP-MCP. As a result, many data concerning with HP-MCP are gained and the conclusions indicate: the HP-MCP can be applied in Gen III Image Intensifier, and can manufacture qualified product; thinking over batch production in the future, studying on the MCP' material and technique especially in compatibility between HP MCP and Gen III image intensifier is enhanced.

  13. LiGen: a high performance workflow for chemistry driven de novo design.

    PubMed

    Beccari, Andrea R; Cavazzoni, Carlo; Beato, Claudia; Costantino, Gabriele

    2013-06-24

    Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented. PMID:23617275

  14. Archaeoditomotarsus crassitylus, gen. and sp. nov. (Hemiptera: Heteroptera: Acanthosomatidae) from Chile.

    PubMed

    Faúndez, Eduardo I; Carvajal, Máriom A; Rider, David A

    2014-01-01

    Archaeoditomotarsus crassitylus, gen. and sp. nov. of Acanthosomatidae (Ditomotarsinae: Ditomotarsini), is described and illustrated. The biogeography of the new taxon is discussed and a key to the Chilean genera of Ditomotarsinae is included.  PMID:25283192

  15. GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation

    PubMed Central

    Gosink, Mark; Khuri, Sawsan; Valdes, Camilo; Jiang, Zhijie; Tsinoremas, Nicholas F.

    2011-01-01

    The GenSensor Suite consists of four web tools for elucidating relationships among genes and proteins. GenPath results show which biochemical, regulatory, or other gene set categories are over- or under-represented in an input list compared to a background list. All common gene sets are available for searching in GenPath, plus some specialized sets. Users can add custom background lists. GenInteract builds an interaction gene list from a single gene input and then analyzes this in GenPath. GenPubMed uses a PubMed query to identify a list of PubMed IDs, from which a gene list is extracted and queried in GenPath. GenViewer allows the user to query one gene set against another in GenPath. GenPath results are presented with relevant P- and q-values in an uncluttered, fully linked, and integrated table. Users can easily copy this table and paste it directly into a spreadsheet or document. PMID:22194743

  16. GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation.

    PubMed

    Gosink, Mark; Khuri, Sawsan; Valdes, Camilo; Jiang, Zhijie; Tsinoremas, Nicholas F

    2011-01-01

    The GenSensor Suite consists of four web tools for elucidating relationships among genes and proteins. GenPath results show which biochemical, regulatory, or other gene set categories are over- or under-represented in an input list compared to a background list. All common gene sets are available for searching in GenPath, plus some specialized sets. Users can add custom background lists. GenInteract builds an interaction gene list from a single gene input and then analyzes this in GenPath. GenPubMed uses a PubMed query to identify a list of PubMed IDs, from which a gene list is extracted and queried in GenPath. GenViewer allows the user to query one gene set against another in GenPath. GenPath results are presented with relevant P- and q-values in an uncluttered, fully linked, and integrated table. Users can easily copy this table and paste it directly into a spreadsheet or document. PMID:22194743

  17. Genes and proteins of Escherichia coli K-12 (GenProtEC).

    PubMed

    Riley, M

    1997-01-01

    GenProtEC is a database of Escherichia coli genes and their gene products, classified by type of function and physiological role and with citations to the literature for each. Also present are data on sequence similarities amongE.coliproteins with PAM values, percent identity of amino acids, length of alignment and percent aligned. GenProtEC can also be accessed through the World Wide Web at URL http://mbl.edu/html/ecoli.html . PMID:9016503

  18. Preliminary Investigation of Civil Tiltrotor in NextGen Airspace

    NASA Technical Reports Server (NTRS)

    Young, Larry A.; Salvano, Dan; Wright, Ken; Chung, William; Young, Ray; Miller, David; Paris, Alfanso; Gao, Huina; Cheng, Victor

    2010-01-01

    Presentation intro: Tiltrotor aircraft have long been envisioned as being a potentially viable means of commercial aviation transport. Preliminary results from an ongoing study into the operational and technological considerations of Civil Tiltrotor (CTR) operation in the Next Generation airspace, circa the 2025 time-frame, are presented and discussed. In particular, a fleet of CTR aircraft has been conceptually designed. The performance characteristics of this CTR fleet was subsequently translated into BADA (Base of Aircraft DAta) models that could be used as input to emulate CTR aircraft operations in the ACES and AvTerminal airspace and terminal area simulation tools. A network of nine North-Eastern corridor airports is the focus of the airspace simulation effort; the results from this airport network viII then be extrapolated to provide insights into systemic impact of CTRs on the National Airspace System (NAS). Future work will also be detailed as to attempts to model the systemic effects of noise and emissions from this fleet of new aircraft as well as assess their leveraged impact on public service missions, in time of need, such as major regional/national disaster relief efforts. The ideal outcome of this study is a set of results whereby Next Gen airspace CONOPs can be refined to reflect potential CTR capabilities and, conversely, CTR technology development efforts can be better informed as to key performance requirement thresholds needed to be met in order to successfully introduce these aircraft into civilian aviation operation.

  19. Eisenbergiella tayi gen. nov., sp. nov., isolated from human blood.

    PubMed

    Amir, Itay; Bouvet, Philippe; Legeay, Christine; Gophna, Uri; Weinberger, Abraham

    2014-03-01

    A catalase-positive, rod-shaped, non-proteolytic, non-motile, anaerobic bacterial strain, designated B086562(T), was isolated from a blood culture of an 84-year-old male patient in Israel. According to 16S rRNA gene sequence phylogeny, this strain has no known close relatives among recognized bacteria but should be placed within the family Lachnospiraceae. The most closely related recognized bacteria were from the 'Clostridium clostridioforme group': C. clostridioforme (92.4%) and Clostridium bolteae (92.3%). The isolate produced butyrate, lactate, acetate and succinate as major metabolic end products. The major fatty acids were C16:0 and C18:1 cis 9 DMA and the DNA G+C content was 46.0 mol%. On the basis of the phenotypic properties and phylogenetic distinctiveness, the blood isolate represents a novel species of a new genus in the family Lachnospiraceae, for which the name Eisenbergiella tayi gen. nov., sp. nov. is proposed. The type strain of Eisenbergiella tayi is B086562(T) (?=?LMG 27400(T)?=?DSM 26961(T)?=?ATCC BAA-2558(T)). PMID:24282142

  20. Youhaiella tibetensis gen. nov., sp. nov., isolated from subsurface sediment.

    PubMed

    Wang, Yun-xiang; Huang, Fa-qi; Nogi, Yuichi; Pang, Shou-Ji; Wang, Ping-kang; Lv, Jie

    2015-07-01

    A Gram-reaction-negative bacterial strain, designated fig4(T), was isolated from a subsurface sediment core of Qiangtang Basin permafrost in China. Cells were catalase- and oxidase-positive and rods. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain fig4(T )was a member of the family Hyphomicrobiaceae and was most closely related to members of the genera Pelagibacterium, Vasilyevaea and Devosia with 93.8-96.2% sequence similarities. The major cellular fatty acids were C16 : 0, C18 : 0, 11-methyl C18 : 1 ?7c, C19 : 0 cyclo ?8c and summed feature 8 (C18 : 1?7c and/or C18 : 1?6c). The major respiratory quinone was Q-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The DNA G+C content was 60.7 mol%. Based on the phenotypic, phylogenetic and genotypic data, strain fig4(T) is considered to represent a novel species of a new genus in the family Hyphomicrobiaceae, for which the name Youhaiella tibetensis gen. nov., sp. nov. is proposed. The type strain is fig4(T) (?=?CGMCC 1.12719(T) = JCM 19854(T)). PMID:25829329

  1. Safety Sufficiency for NextGen: Assessment of Selected Existing Safety Methods, Tools, Processes, and Regulations

    NASA Technical Reports Server (NTRS)

    Xu, Xidong; Ulrey, Mike L.; Brown, John A.; Mast, James; Lapis, Mary B.

    2013-01-01

    NextGen is a complex socio-technical system and, in many ways, it is expected to be more complex than the current system. It is vital to assess the safety impact of the NextGen elements (technologies, systems, and procedures) in a rigorous and systematic way and to ensure that they do not compromise safety. In this study, the NextGen elements in the form of Operational Improvements (OIs), Enablers, Research Activities, Development Activities, and Policy Issues were identified. The overall hazard situation in NextGen was outlined; a high-level hazard analysis was conducted with respect to multiple elements in a representative NextGen OI known as OI-0349 (Automation Support for Separation Management); and the hazards resulting from the highly dynamic complexity involved in an OI-0349 scenario were illustrated. A selected but representative set of the existing safety methods, tools, processes, and regulations was then reviewed and analyzed regarding whether they are sufficient to assess safety in the elements of that OI and ensure that safety will not be compromised and whether they might incur intolerably high costs.

  2. Initial Investigation of Operational Concept Elements for NASA's NextGen-Airportal Project Research

    NASA Technical Reports Server (NTRS)

    Lohr, Gary; Lee, Jonathan; Poage, James L.; Tobias, Leonard

    2009-01-01

    The NextGen-Airportal Project is organized into three research focus areas: Safe and Efficient Surface Operations, Coordinated Arrival/Departure Operations Management, and Airportal Transition and Integration Management. The content in this document was derived from an examination of constraints and problems at airports for accommodating future increases in air traffic, and from an examination of capabilities envisioned for NextGen. The concepts are organized around categories of constraints and problems and therefore do not precisely match, but generally reflect, the research focus areas. The concepts provide a framework for defining and coordinating research activities that are, and will be, conducted by the NextGen-Airportal Project. The concepts will help the research activities function as an integrated set focused on future needs for airport operations and will aid aligning the research activities with NextGen key capabilities. The concepts are presented as concept elements with more detailed sub-elements under each concept element. For each concept element, the following topics are discussed: constraints and problems being addressed, benefit descriptions, required technology and infrastructure, and an initial list of potential research topics. Concept content will be updated and more detail added as the research progresses. The concepts are focused on enhancing airportal capacity and efficiency in a timeframe 20 to 25 years in the future, which is similar to NextGen's timeframe.

  3. Critical Issues on Materials for Gen-IV Reactors

    SciTech Connect

    Caro, M; Marian, J; Martinez, E; Erhart, P

    2009-02-27

    Within the LDRD on 'Critical Issues on Materials for Gen-IV Reactors' basic thermodynamics of the Fe-Cr alloy and accurate atomistic modeling were used to help develop the capability to predict hardening, swelling and embrittlement using the paradigm of Multiscale Materials Modeling. Approaches at atomistic and mesoscale levels were linked to build-up the first steps in an integrated modeling platform that seeks to relate in a near-term effort dislocation dynamics to polycrystal plasticity. The requirements originated in the reactor systems under consideration today for future sources of nuclear energy. These requirements are beyond the present day performance of nuclear materials and calls for the development of new, high temperature, radiation resistant materials. Fe-Cr alloys with 9-12% Cr content are the base matrix of advanced ferritic/martensitic (FM) steels envisaged as fuel cladding and structural components of Gen-IV reactors. Predictive tools are needed to calculate structural and mechanical properties of these steels. This project represents a contribution in that direction. The synergy between the continuous progress of parallel computing and the spectacular advances in the theoretical framework that describes materials have lead to a significant advance in our comprehension of materials properties and their mechanical behavior. We took this progress to our advantage and within this LDRD were able to provide a detailed physical understanding of iron-chromium alloys microstructural behavior. By combining ab-initio simulations, many-body interatomic potential development, and mesoscale dislocation dynamics we were able to describe their microstructure evolution. For the first time in the case of Fe-Cr alloys, atomistic and mesoscale were merged and the first steps taken towards incorporating ordering and precipitation effects into dislocation dynamics (DD) simulations. Molecular dynamics (MD) studies of the transport of self-interstitial, vacancy and point defect clusters in concentrated Fe-Cr alloys were performed for future diffusion data calculations. A recently developed parallel MC code with displacement allowed us to predict the evolution of the defect microstructures, local chemistry changes, grain boundary segregation and precipitation resulting from radiation enhanced diffusion. We showed that grain boundaries, dislocations and free surfaces are not preferential for alpha-prime precipitation, and explained experimental observations of short-range order (SRO) in Fe-rich FeCr alloys. Our atomistic studies of dislocation hardening allowed us to obtain dislocation mobility functions for BCC pure iron and Fe-Cr and determine for FCC metals the dislocation interaction with precipitates with a description to be used in Dislocation Dynamic (DD) codes. A Synchronous parallel Kinetic Monte Carlo code was developed and tested which promises to expand the range of applicability of kMC simulations. This LDRD furthered the limits of the available science on the thermodynamic and mechanic behavior of metallic alloys and extended the application of physically-based multiscale materials modeling to cases of severe temperature and neutron fluence conditions in advanced future nuclear reactors. The report is organized as follows: after a brief introduction, we present the research activities, and results obtained. We give recommendations on future LLNL activities that may contribute to the progress in this area, together with examples of possible research lines to be supported.

  4. Oryzobacter terrae gen. nov., sp. nov., isolated from paddy soil.

    PubMed

    Kim, Soo-Jin; Lim, Jun-Muk; Hamada, Moriyuki; Ahn, Jae-Hyung; Weon, Hang-Yeon; Suzuki, Ken-ichiro; Ahn, Tae-Young; Kwon, Soon-Wo

    2015-09-01

    A bacterial strain, PSGM2-16(T), was isolated from a pot of paddy soil grown with rice in Suwon region, Republic of Korea, and was characterized as having aerobic, Gram-stain-positive, short-rod-shaped cells with one polar flagellum. The 16S rRNA gene sequence of strain PSGM2-16(T) revealed the highest sequence similarities with Knoellia locipacati DMZ1T (97.4%), Fodinibacter luteus YIM C003(T) (97.2%) and Lapillicoccus jejuensis R-Ac013(T) (97.0%), and the phylogenetic tree showed that strain PSGM2-16(T) formed a subgroup with Ornithinibacter aureus HB09001(T) and F. luteus YIM C003(T) within the family Intrasporangiaceae. The major fatty acids (>10% of the total fatty acids) of strain PSGM2-16(T) were iso-C16 : 0, C17 : 1?8c and iso-C14 : 0. The predominant menaquinone was MK-8(H4). The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, three aminophospholipids and two phospholipids. The peptidoglycan was type A4? with meso-diaminopimelic acid as the diagnostic diamino acid. DNA-DNA hybridization values between strain PSGM2-16(T) and closely related taxa were much less than 70%. The genomic DNA G+C content of strain PSGM2-16(T) was 70.0 mol%. On the basis of the evidence presented, it is concluded that strain PSGM2-16(T) represents a novel species of a new genus in the family Intrasporangiaceae, for which the name Oryzobacter terrae gen. nov., sp. nov. is proposed. The type strain of the type species is PSGM2-16(T) (?= KACC 17299(T)= DSM 27137(T)= NBRC 109598(T)). PMID:26297674

  5. Chujaibacter soli gen. nov., sp. nov., isolated from soil.

    PubMed

    Kim, Soo-Jin; Ahn, Jae-Hyung; Weon, Hang-Yeon; Hong, Seung-Beom; Seok, Soon-Ja; Kim, Jeong-Seon; Kwon, Soon-Wo

    2015-09-01

    A Gram-staining-negative, aerobic, non-flagellated, rod-shaped bacterial strain, KIS55-21(T), was isolated from a soil sample from Chuja Island, Jeju Province, Republic of Korea. Strain KIS55-21(T) grew optimally at pH 7.0, at 28-30C and in the presence of 0% (w/v) NaCl. Neighbor-joining and maximum-likelihood trees based on the 16S rRNA gene sequences revealed that strain KIS55-21(T) fell within the family Xanthomonadaceae and was closely related to Metallibacterium scheffleri DKE(T). Strain KIS55-21(T) exhibited the highest 16S rRNA gene sequence similarity (92.6%) to that of M. scheffleri DKE(T), with similarities of less than 92.0% to those of the genera Dokdonella, Rhodanobacter, Aquimonas, and Frateuria. Strain KIS55-21(T) contained ubiquinone-8 (Q-8) as the predominant ubiquinone, iso-C17:0, summed feature 9 (iso-C17:1 ?9c and/or C16:0 10-methyl), anteiso-C17:0 and C16:0 as the major fatty acids, and phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylmonomethylethanolamine as the main polar lipids. The DNA G+C content of strain KIS55-21(T) was 65.9 mol%. Differential phenotypic and chemotaxonomic properties and phylogenetic data of strain KIS55-21(T) demonstrated that this strain is distinguishable from closely related genera within the family Xanthomonadaceae. On the basis of the data presented, strain KIS55-21(T) is considered to represent a novel genus and species, for which the name Chujaibacter soli gen. nov., sp. nov. is proposed. The type strain is KIS55-21(T) (=KACC 16971(T) =DSM 28578(T)). PMID:26310302

  6. Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater.

    PubMed

    Kim, Min-Kyeong; Kim, Tae-Woon; Kim, Tae-Su; Joung, Yochan; Han, Ji-Hye; Kim, Seung Bum

    2016-01-01

    A Gram-stain-negative, non-spore-forming and coccus-shaped bacterial strain, designated 4DR5T, was isolated from freshwater and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-40?C (optimum 30?C), at pH?6-9 (optimum pH?7) and in the presence of 0-0.4?% (w/v) NaCl (optimum 0?%) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain 4DR5T was assigned to the family Moraxellaceae of the class Gammaproteobacteria, and its closest related taxa were species of the genera Perlucidibaca (93.67?% sequence similarity), Agitococcus (93.07?%), Paraperlucidibaca (92.31-92.38?%), Alkanindiges (91.79?%) and Acinetobacter (90.24-91.23?%). The predominant isoprenoid quinone detected in strain 4DR5T was Q-10. The major cellular fatty acids were a summed feature consisting of C16?:?1?7c and/or C16?:?1?6c, one consisting of C18?:?1?7c and/or C18?:?1?6c, and C16?:?0. The major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of the strain was 61.2?mol%. The phylogenetic, chemotaxonomic and biochemical data not only supported the affiliation of strain 4DR5T to the family Moraxellaceae, but also separated it from other established genera within the family. Therefore, the novel isolate evidently represents a novel species of a new genus of Moraxellaceae, for which the name Fluviicoccus keumensis gen. nov., sp. nov. is proposed. The?type strain of Fluviicoccus keumensis is 4DR5T (?=?KCTC 32475T?=?JCM 19370T). PMID:26498187

  7. Fusicatenibacter saccharivorans gen. nov., sp. nov., isolated from human faeces.

    PubMed

    Takada, Toshihiko; Kurakawa, Takashi; Tsuji, Hirokazu; Nomoto, Koji

    2013-10-01

    Three Gram-stain-positive, obligately anaerobic, non-motile, non-spore-forming, spindle-shaped bacterial strains (HT03-11(T), KO-38 and TT-111), isolated from human faeces were characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were highly related to each other genetically (displaying >99?% sequence similarity) and represented a previously unknown subline within the Blautia coccoides rRNA group of organisms (cluster XIVa). The closest phylogenetic neighbours of strain HT03-11(T) were Clostridium bolteae WAL 16351(T) (93.7?% 16S rRNA gene sequence similarity) and Clostridium saccharolyticum WM1(T) (93.7?% similarity). All isolates produced lactic acid, formic acid, acetic acid and succinic acid as fermentation end products from glucose. Their chemotaxonomic properties included lysine as the cell wall diamino acid and C16?:?0, C18?:?1?7c DMA and C16?:?0 DMA as the major fatty acids. The G+C contents of the genomic DNA were 46.9-47.2 mol% (HPLC). Several phenotypic and chemotaxonomic characteristics could be readily used to differentiate the isolates from phylogenetically related clostridia. Therefore, strains HT03-11(T), KO-38 and TT-111 represent a novel species in a new genus of the family Lachnospiraceae, for which the name Fusicatenibacter saccharivorans gen. nov., sp. nov. is proposed. The type strain of the type species is HT03-11(T) (?=?YIT 12554(T)?=?JCM 18507(T)?=?DSM 26062(T)). PMID:23625266

  8. Design and manufacturing of 10G GenX VCSELs at Emcore

    NASA Astrophysics Data System (ADS)

    Li, Nein-Yi; Collins, Doug; Jatar, Shashank; Lavrova, Olga; Helms, Chris; Luo, Wenlin; Liu, Linlin; Liu, Chiyu; Qiu, Mei; Roff, Kent; Wang, Charlie; Yang, Chia-Chun; Chiou, Hwann-Kaeo

    2007-02-01

    In this paper, we present the design and manufacturing of next-generation 850 nm 10 Gb/s vertical-cavity surface-emitting lasers (GenX VCSELs). They were developed to provide a 10 Gb/s solution that meets Class-1 eye safety limits, IEEE 802.3ae standards, 10G Fiber Channel standards, and corresponding multisource agreement requirements for emerging low-cost, high-volume, and high-performance data communication applications in local and storage area networks (LANs and SANs). The paper covers GenX device designs, manufacturing processes, DC and AC characteristics, equivalent circuit models, recommended operating conditions, as well as reliability studies. As a simple drop-in replacement, we have successfully demonstrated that GenX VCSELs work well with all existing Emcore 10G transmitter optical sub-assembly (TOSA) products.

  9. Tools for Designing, Evaluating, and Certifying NextGen Technologies and Procedures: Automation Roles and Responsibilities

    NASA Technical Reports Server (NTRS)

    Kanki, Barbara G.

    2011-01-01

    Barbara Kanki from NASA Ames Research Center will discuss research that focuses on the collaborations between pilots, air traffic controllers and dispatchers that will change in NextGen systems as automation increases and roles and responsibilities change. The approach taken by this NASA Ames team is to build a collaborative systems assessment template (CSAT) based on detailed task descriptions within each system to establish a baseline of the current operations. The collaborative content and context are delineated through the review of regulatory and advisory materials, policies, procedures and documented practices as augmented by field observations and interviews. The CSAT is developed to aid the assessment of key human factors and performance tradeoffs that result from considering different collaborative arrangements under NextGen system changes. In theory, the CSAT product may be applied to any NextGen application (such as Trajectory Based Operations) with specified ground and aircraft capabilities.

  10. Discourses in Conflict: The Relationship between Gen Y Pre-Service Teachers, Digital Technologies and Lifelong Learning

    ERIC Educational Resources Information Center

    Donnison, Sharn

    2009-01-01

    This paper analyses Gen Y pre-service primary school teachers' conceptualisations of lifelong learning. It is situated within a context of improving the provision and delivery of pre-service teacher education. This paper argues that Gen Y's understanding of lifelong learning has been influenced by their engagements with digital technologies and

  11. Complete cDNAs from Nylanderia cf. pubens (Hymenoptera: Formicidae). --GenBank accession numbers: JF815100-JF815104

    Technology Transfer Automated Retrieval System (TEKTRAN)

    5 new gene sequences were identified from workers of Caribbean crazy ant, Nylanderia cf. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are JF815100-JF815104. This information will provide scientists with genetic tools to study the popu...

  12. 75 FR 35018 - GenConn Energy LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-21

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission GenConn Energy LLC; Supplemental Notice That Initial Market-Based Rate... notice in the above-referenced proceeding of GenConn Energy LLC's application for market-based...

  13. 75 FR 80488 - Notice of Cancellation of Environmental Impact Statement for the Proposed NextGen Project Near...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-22

    ... Register on July 27, 2007 (72 FR 41307). Public scoping meetings were held subsequent to the Notice of... NextGen Project Near Selby, Walworth County, SD (DOE/EIS-0401) AGENCY: Western Area Power..., South Dakota. BEPC's proposed NextGen Project would have been entirely owned and operated by BEPC,...

  14. 75 FR 80487 - Cambria CoGen Company; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-22

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Cambria CoGen Company; Supplemental Notice That Initial Market- Based Rate... notice in the above-referenced proceeding of Cambria CoGen Company's application for market-based...

  15. 77 FR 56839 - GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission GenOn Marsh Landing, LLC; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding, of GenOn Marsh Landing, LLC's application for market-based rate authority, with...

  16. 78 FR 49507 - OriGen Energy LLC ; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-14

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission OriGen Energy LLC ; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding of OriGen Energy LLC's application for market-based rate authority, with...

  17. 78 FR 77670 - AlphaGen Power LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes Request...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission AlphaGen Power LLC; Supplemental Notice That Initial Market-Based Rate...-referenced proceeding, of AlphaGen Power LLC's application for market-based rate authority, with...

  18. Discourses in Conflict: The Relationship between Gen Y Pre-Service Teachers, Digital Technologies and Lifelong Learning

    ERIC Educational Resources Information Center

    Donnison, Sharn

    2009-01-01

    This paper analyses Gen Y pre-service primary school teachers' conceptualisations of lifelong learning. It is situated within a context of improving the provision and delivery of pre-service teacher education. This paper argues that Gen Y's understanding of lifelong learning has been influenced by their engagements with digital technologies and…

  19. Complete cDNAs from Brachymyrmex patagonicus (Hymenoptera: Formicidae). --GenBank accession numbers: GU582126-GU582140.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    15 new gene sequences were identified from workers of Brachymyrmex patagonicus, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU582126-GU582140. This information will provide scientists with genetic tools to study the development and the p...

  20. Complete cDNAs from Nylanderia sp. nr. pubens (Hymenoptera: Formicidae). GenBank GU980916-GU980928.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    13 new gene sequences were identified from workers of Rasberry crazy ant, Nylanderia sp.nr. pubens, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are GU980916-GU980928. This information will provide scientists with genetic tools to study the p...

  1. Complete cDNAs from Solenopsis invicta (Hymenoptera: Formicidae). --GenBank accession numbers: HM130684-HM130685.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    2 new gene sequences were identified from workers of Solenopsis invicta, and submitted to the National Center for Biotechnology Information GenBank. GenBank accession numbers are HM130684-HM130685. This information will provide scientists with genetic tools to study the populations of this ant....

  2. HIV gp120 vaccine - VaxGen: AIDSVAX, AIDSVAX B/B, AIDSVAX B/E, HIV gp120 vaccine - Genentech, HIV gp120 vaccine AIDSVAX - VaxGen, HIV vaccine AIDSVAX - VaxGen.

    PubMed

    2003-01-01

    VaxGen is developing prophylactic vaccines against HIV-1 consisting of two recombinant gp120 surface proteins from different HIV-1 strains.This profile has been selected from R&D Insight, a pharmaceutical intelligence database produced by Adis International Ltd. The bivalent vaccines [AIDSVAX B/B and AIDSVAX B/E] are being evaluated in two phase III trials. The first multicentre phase III trial of AIDSVAX B/B, was conducted principally in Canada and the US but also at some sites in the Netherlands and Puerto Rico. The trial was completed at the end of 2002. The second phase III trial is being conducted in Thailand with the AIDSVAX B/E vaccine. VaxGen announced in July 2002 that it would be delaying its Biologics License Application (BLA) for AIDSVAX until 2004 to enable the company to fulfil pre-approval manufacturing requirements. AIDSVAX is based on an earlier monovalent gp120 vaccine developed by Genentech that was shown to be safe in humans. VaxGen (formerly Genenvax) was formed as a spin-off company from Genentech with the sole purpose of developing the gp120 vaccine. VaxGen announced in July 2002 that the original License and Supply agreement with Genentech, signed in May 1997, had been amended. Under the revised agreement, Genentech maintains its right to market and sell AIDSVAX in North America, but has relinquished its options to commercialise the vaccine candidate in the rest of the world. Genentech's earlier decision to waive its option to manufacture AIDSVAX has also been formalised in this agreement. Additionally, VaxGen's royalty payments to Genentech for sales to the WHO or UN for underdeveloped nations have also been reduced by up to 50% and Genentech has extended the milestone date associated with VaxGen submitting an NDA. A $US120 million joint venture (Celltrion) has been formed between VaxGen and South Korean investors to manufacture more than 200 million doses of AIDSVAX a year. Celltrion will build and operate two biotechnology manufacturing facilities: a pilot plant in South San Francisco and a larger plant in Incheon, South Korea. VaxGen will retain a 44% interest in the new company, as well as any profit generated by the AIDS vaccine. If AIDSVAX wins regulatory approval, VaxGen is committed to purchasing a minimum of 87 million doses a year. Celltrion announced in July 2002 that it had acquired 24 acres of land in Incheon, South Korea, for the site of its major biologics manufacturing facility. The facility is scheduled to be ready for commercial operation by 2005. The US FDA granted fast-track designations to the two vaccines AIDSVAX B/B and AIDSVAX B/E in December 2002. The study volunteers included 5108 men who have sex with men and 309 at-risk women, all of whom were meant to be HIV negative when they joined the trial. During the 36-month trial, a total of seven injections were administered at months 0, 1, 6, 12, 18, 24 and 30. The ratio of vaccine to placebo recipients was 2:1. On February 24 2003, VaxGen announced that AIDSVAX B/B did not prove effective in the trials conducted in North America and Europe. The study did not show a statistically significant reduction of HIV infection within the study population as a whole, which was the primary endpoint of the trial. However, the study did show a statistically significant reduction of HIV infection in certain vaccinated groups. Trial data indicate that black and Asian volunteers appeared to produce higher levels of antibodies against HIV. White and Hispanic volunteers appeared to develop consistently lower levels of protective antibodies following vaccination. VaxGen intends to conduct additional analyses to confirm if there was a direct correlation between the level of antibodies and the prevention of infection. The company intends to continue development of the vaccine through licensure, including any studies necessary to evaluate the protective riticism in the media about the statistical analysis of the non-Caucasian data, VaxGen issued a statement on 27 February 2003 claiming that the analysis of data from the trial followed a statistical analysis plan that was agreed on in advance with the US FDA. The plan included analyses of various subgroups, including racial backgrounds. Subsequently, VaxGen presented further analyses of the phase III data at the Keystone Symposia on 31 March 2003, and stated that the differences in vaccine efficacy observed between the Caucasian and non-Caucasian (Black, Asian and other) vaccinees could not have been due solely to chance. In May 2003, VaxGen stated that it would only continue developing AIDSVAX if government agencies and philanthropic organisations provide the necessary funding. AIDSVAX B/E is designed to protect against strains of HIV-1 prevalent in Indonesia, Japan, Korea, Taiwan and Thailand. Like the North American study, this trial also includes an interim efficacy analysis, set for 24 months after completion of enrolment. Results from this trial are expected to be announced in the second half of 2003. This trial received its final favourable review from the DSMB in October 2002. Based on this result, the National Institute of Allergy and Infectious Disease (NIAID) has decided to pursue only one of the two previously planned phase III trials involving immunisation with vCP1452 and AIDSVAX B/B. The NIAID will not conduct the North and South American phase III trial. It will, however, proceed with the planned 'prime-boost' phase III trial in Thailand, to evaluate the efficacy of a similar vaccine combination, ALVAC-HIV-vCP1521 and AIDSVAX B/E, both of which incorporate envelope antigens from the predominant circulating HIV (CRF_AE_01) in Thailand. The trial is expected to begin enrolling volunteers in March 2003. VaxGen was a awarded $US3.3 million contract to supply AIDSVAX B/E for the trial, which will be funded by the NIH and conducted by the US Army. NIAID and the HIV Trials Network (HVTN) are conducting a phase II trial (HVTN 026), testing the immunogenicity of vCP1452 alone and in combination with AIDSVAX among populations in Brazil, Haiti, Peru and Trinidad and Tobago. PMID:12848591

  3. Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov.

    PubMed Central

    Lagier, Jean-Christophe; Elkarkouri, Khalid; Rivet, Romain; Couderc, Carine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaerobia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein-coding and 58 RNA genes. PMID:24019984

  4. Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut

    PubMed Central

    Tidjani Alou, M.; Rathored, J.; Lagier, J.-C.; Khelaifia, S.; Labas, N.; Sokhna, C.; Diallo, A.; Raoult, D.; Dubourg, G.

    2016-01-01

    Massilibacterium senegalense gen. nov., sp. nov., strain mt8T, is the type strain of Massilibacterium gen. nov., a new genus within the Bacillaceae family. This Gram-negative facultative anaerobic rod was isolated from the gut microbiota of a severely malnourished boy. Its phenotypic description is hereby presented with a complete annotation of its genome sequence. This genome is 5 697 950 bp long and contains 5615 protein-coding genes and 178 RNA genes, among which are 40 rRNA genes. PMID:26933503

  5. 75 FR 27332 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources, LLC; Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-14

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC; Eagle Creek Water Resources... Comments and Motions To Intervene May 7, 2010. On April 30, 2010, AER NY-Gen, LLC (transferor) and Eagle.... Joseph Klimaszewski, AER NY- Gen, LLC, 613 Plank Road, Forestburgh, New York, 12777; phone (845)...

  6. 77 FR 13592 - AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources, LLC, Eagle Creek Land...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-07

    ... Energy Regulatory Commission AER NY-Gen, LLC; Eagle Creek Hydro Power, LLC, Eagle Creek Water Resources... Comments and Motions To Intervene On February 24, 2012, AER NY-Gen, LLC (transferor), Eagle Creek Hydro...' Contact: Transferor: Mr. Joseph Klimaszewski, AER NY- Gen, LLC, P.O. Box 876, East Aurora, NY 14052,...

  7. Novel anamorphic mite-associated fungi belonging to the Ustilaginomycetes: Meira geulakonigii gen. nov., sp. nov., Meira argovae sp. nov. and Acaromyces ingoldii gen. nov., sp. nov.

    PubMed

    Boekhout, Teun; Theelen, Bart; Houbraken, Jos; Robert, Vincent; Scorzetti, Gloria; Gafni, Aviva; Gerson, Uri; Sztejnberg, Abraham

    2003-09-01

    Three novel mite-associated basidiomycetous species are described in two new anamorph genera as Meira geulakonigii gen. nov., sp. nov. (type CBS 110052(T)=NRRL Y-27483(T)=AS 004(T)), Meira argovae sp. nov. (type CBS 110053(T)=NRRL Y-27482(T)=AS 005(T)) and Acaromyces ingoldii gen. nov., sp. nov. (type CBS 110050(T)=NRRL Y-27484(T)=AS 001(T)). Morphologically, these fungi are similar to the yeast-like fungi classified in the Ustilaginales, such as Pseudozyma species. However, analysis of the D1/D2 domain of the LSU rDNA suggests that they belong to two different lineages within the Exobasidiomycetidae of the Ustilaginomycetes (Basidiomycota). Furthermore, these fungi may be of interest for the biocontrol of mites, as they reduced mite numbers by approximately 80 % after inoculation. PMID:13130065

  8. GenMin: An enhanced genetic algorithm for global optimization

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, I. E.

    2008-06-01

    A new method that employs grammatical evolution and a stopping rule for finding the global minimum of a continuous multidimensional, multimodal function is considered. The genetic algorithm used is a hybrid genetic algorithm in conjunction with a local search procedure. We list results from numerical experiments with a series of test functions and we compare with other established global optimization methods. The accompanying software accepts objective functions coded either in Fortran 77 or in C++. Program summaryProgram title: GenMin Catalogue identifier: AEAR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAR_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 35 810 No. of bytes in distributed program, including test data, etc.: 436 613 Distribution format: tar.gz Programming language: GNU-C++, GNU-C, GNU Fortran 77 Computer: The tool is designed to be portable in all systems running the GNU C++ compiler Operating system: The tool is designed to be portable in all systems running the GNU C++ compiler RAM: 200 KB Word size: 32 bits Classification: 4.9 Nature of problem: A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques are frequently trapped in local minima. Global optimization is hence the appropriate tool. For example, solving a nonlinear system of equations via optimization, employing a least squares type of objective, one may encounter many local minima that do not correspond to solutions (i.e. they are far from zero). Solution method: Grammatical evolution and a stopping rule. Running time: Depending on the objective function. The test example given takes only a few seconds to run.

  9. Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash.

    PubMed

    Lee, Dong Wan; Lee, Soon Dong

    2011-02-01

    A novel actinomycete, designated strain Sco-B14(T), was isolated from volcanic ash collected near Darangshi Oreum (a parasitic or satellite volcano) in Jeju, Republic of Korea. The organism formed well-developed, branched substrate mycelium, on which short chains of non-motile spores were arranged singly or in clusters. Aerial mycelium was not produced. Globose bodies were observed. The reverse colour of colonies was light brown to brown. Diffusible pigments were produced on ISP medium 3 and oatmeal-nitrate agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Sco-B14(T) formed a lineage within the family Micromonosporaceae and was distinct from established genera. The 16S rRNA gene sequence similarity of strain Sco-B14(T) to members of related genera of the family was 95.0-95.7?% to type strains of Catellatospora species, 94.7?% to Hamadaea tsunoensis IMSNU 22005(T), 94.7?% to Longispora albida K97-0003(T) and 94.0?% to Catelliglobosispora koreensis LM 042(T). 3-Hydroxydiaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Whole-cell sugars were glucose, rhamnose, ribose, xylose, arabinose, galactose and mannose. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The menaquinone profile contained MK-10(H(4)) (49?%), MK-9(H(4)) (24?%), MK-10(H(6)) (18?%) and MK-9(H(6)) (9?%). The predominant fatty acids were iso-C(15?:?0) and C(17?:?0). The DNA G+C content was 70.1 mol%. The combination of chemotaxonomic and phylogenetic data clearly separated the isolate from the type strains of all genera in the family Micromonosporaceae. On the basis of the phylogenetic and chemotaxonomic data presented in this paper, strain Sco-B14(T) is considered to represent a novel species of a new genus in the family Micromonosporaceae, for which the name Allocatelliglobosispora scoriae gen. nov., sp. nov. is proposed. The type strain of Allocatelliglobosispora scoriae is Sco-B14(T) (=KCTC 19661(T) =DSM 45362(T)). PMID:20207801

  10. NextGen Operations in a Simulated NY Area Airspace

    NASA Technical Reports Server (NTRS)

    Smith, Nancy M.; Parke, Bonny; Lee, Paul; Homola, Jeff; Brasil, Connie; Buckley, Nathan; Cabrall, Chris; Chevalley, Eric; Lin, Cindy; Morey, Susan; Omar, Faisal; Rein-Weston, Daphne; Yoo, Hyo-Sang

    2013-01-01

    A human-in-the-loop simulation conducted in the Airspace Operations Laboratory (AOL) at NASA Ames Research Center explored the feasibility of a Next Generation Air Transportation System (NextGen) solution to address airspace and airport capacity limitations in and around the New York metropolitan area. A week-long study explored the feasibility of a new Optimal Profile Descent (OPD) arrival into the airspace as well as a novel application of a Terminal Area Precision Scheduling and Spacing (TAPSS) enhancement to the Traffic Management Advisor (TMA) arrival scheduling tool to coordinate high volume arrival traffic to intersecting runways. In the simulation, four en route sector controllers and four terminal radar approach control (TRACON) controllers managed traffic inbound to Newark International Airport's primary runway, 22L, and its intersecting overflow runway, 11. TAPSS was used to generate independent arrival schedules for each runway and a traffic management coordinator participant adjusted the arrival schedule for each runway 11 aircraft to follow one of the 22L aircraft. TAPSS also provided controller-managed spacing tools (slot markers with speed advisories and timelines) to assist the TRACON controllers in managing the arrivals that were descending on OPDs. Results showed that the tools significantly decreased the occurrence of runway violations (potential go-arounds) when compared with a Baseline condition with no tools. Further, the combined use of the tools with the new OPD produced a peak arrival rate of over 65 aircraft per hour using instrument flight rules (IFR), exceeding the current maximum arrival rate at Newark Liberty International Airport (EWR) of 52 per hour under visual flight rules (VFR). Although the participants rated the workload as relatively low and acceptable both with and without the tools, they rated the tools as reducing their workload further. Safety and coordination were rated by most participants as acceptable in both conditions, although the TRACON Runway Coordinator (TRC) rated neither as acceptable in the Baseline condition. Regarding the role of the TRC, the two TRACON controllers handling the 11 arrivals indicated that the TRC was very much needed in the Baseline condition without tools, but not needed in the condition with tools. This indicates that the tools were providing much of the sequencing and spacing information that the TRC had supplied in the Baseline condition.

  11. Halopolyspora alba gen. nov., sp. nov., isolated from sediment.

    PubMed

    Lai, Hangxian; Wei, Xiaomin; Jiang, Yingying; Chen, Xiu; Li, Qinyuan; Jiang, Yi; Jiang, Chenglin; Gillerman, Leionid

    2014-08-01

    A novel halophilic, filamentous actinomycete, designated strain AFM 10251(T), was isolated from a sediment sample collected from the Dead Sea, Israel. The isolate grew with 10-35% multi-salts, and did not grow without NaCl or MgCl2. The isolate formed a white aerial mycelium, and long chains of arthrospores with more than 10 spores per chain. The spores were spherical or oval with warty surfaces, and sterile mycelium was present between individual spores. The isolate contained meso-diaminopimelic acid and a small proportion of LL-diaminopimelic acid as cell-wall diamino acids, and galactose and arabinose as whole-cell sugars. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol and three unknown phospholipids. Major fatty acids were iso-C(16 : 0), iso-C(17 : 0), iso-C(15 : 0) and anteiso-C(17 : 0). The DNA G+C content of strain AFM 10251(T) was 66.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AFM 10251(T) and the genus Actinopolyspora formed a distinct lineage. Analysis of the secondary structures of variable areas of the 16S rRNA gene showed that strain AFM 10251(T) was different from all recognized species of the genus Actinopolyspora and members of the family Pseudonocardiaceae. Analysis of the signature nucleotides of the 16S rRNA gene showed that strain AFM 10251(T) and Actinopolyspora halophila formed a single group, but with base pair differences at positions 127 : 234 and 183 : 194. On the basis of analysis of chemical and molecular characteristics, strain AFM 10251(T) is considered to represent a novel species of a new genus in the family Actinopolysporaceae, for which the name Halopolyspora alba gen. nov., sp. nov. is proposed. The type strain of Halopolyspora alba is AFM 10251(T) ( = DSM 45976(T) = CGMCC 4.7114(T)). PMID:24860112

  12. PZT piezoelectric films on glass for Gen-X imaging

    NASA Astrophysics Data System (ADS)

    Wilke, Rudeger H. T.; Trolier-McKinstry, Susan; Reid, Paul B.; Schwartz, Daniel A.

    2010-09-01

    The proposed adaptive optics system for the Gen-X telescope uses piezoelectric lead zirconate titanate (PZT) films deposited on flexible glass substrates. The low softening transition of the glass substrates imposes several processing challenges that require the development of new approaches to deposit high quality PZT thin films. Synthesis and optimization of chemical solution deposited 1 ?m thick films of PbZr0.52Ti0.48O3 on small area (1 in2) and large area (16 in2) Pt/Ti/glass substrates has been performed. In order to avoid warping of the glass at temperatures typically used to crystallize PZT films ({700C), a lower temperature, two-step crystallization process was employed. An {80 nm thick seed layer of PbZr0.30Ti0.70O3 was deposited to promote the growth of the perovskite phase. After the deposition of the seed layer, the films were annealed in a rapid thermal annealing (RTA) furnace at 550C for 3 minutes to nucleate the perovskite phase. This was followed by isothermal annealing at 550C for 1 hour to complete crystallization. For the subsequent PbZr0.52Ti0.48O3 layers, the same RTA protocol was performed, with the isothermal crystallization implemented following the deposition of three PbZr0.52Ti0.48O3 spin-coated layers. Over the frequency range of 1 kHz to 100 kHz, films exhibit relative permittivity values near 800 with loss tangents below 0.07. Hysteresis loops show low levels of imprint with coercive fields of 40-50 kV/cm in the forward direction and 50-70 kV/cm in the reverse direction. The remanent polarization varied from 25-35 ?C/cm2 and e31,f values were approximately -5.0 C/m2. In scaling up the growth procedure to large area films, where warping becomes more pronounced due to the increased size of the substrate, the pyrolysis and crystallization conditions were performed in a box furnace to improve the temperature uniformity. By depositing films on both sides of the glass substrate, the tensile stresses are balanced, providing a sufficiently flat surface to continue PZT deposition. The properties of the large area film are comparable to those obtained on small substrates. While sol-gel processing is a viable approach to the deposition of high quality PZT thin films on glass substrates, preliminary results using RF magnetron sputter deposition demonstrate comparable properties with a significantly simpler process that offers a superior route for large scale production.

  13. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    PubMed Central

    Liu, Yijin; Freeman, AlasdairD.J.; Dclais, Anne-Ccile; Wilson, TimothyJ.; Gartner, Anton; Lilley, DavidM.J.

    2015-01-01

    Summary We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution.The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of theDNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction. PMID:26686639

  14. GWAS in a box: statistical and visual analytics of structured associations via GenAMap.

    PubMed

    Xing, Eric P; Curtis, Ross E; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  15. FutureGen: Pathway to Near-Zero Emissions and Sustainable Energy

    SciTech Connect

    Zitney, S.E.; Sarkus, T.A

    2007-11-04

    This presentation will highlight the U.S. Department of Energys (DOE) FutureGen project ? a $1 billion government-industry partnership to design, build, and operate a near-zero emissions coal-fueled power plant. The lead organization for the FutureGen initiative is the National Energy Technology Laboratory (NETL), a multi-purpose laboratory operated by the U.S. DOEs Office of Fossil Energy. NETL has a mission to conduct R&D from fundamental science to technology demonstration for resolving the environmental, supply, and reliability constraints of producing and using fossil energy resources. The commercial-scale FutureGen R&D facility is a pathway toward future fossil-energy power plants that will produce hydrogen and electricity while nearly eliminating emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. Low carbon emissions would be achieved by integrating CO2 capture and sequestration operations with the power plant.

  16. List of Predicted Simple Sequence Repeats from Sugar Beet GenBank Accessions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Beta vulgaris ESTs from GenBank as of January 2005 collapsed into 13,618 unique clusters (4,023 Tentative Consensus sequences, 9,595 singletons), and 35% were contributed via work partially supported through the BSDF. These sequences were parsed through SSR-Primer software for discovering potential...

  17. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA.

    PubMed

    Liu, Yijin; Freeman, Alasdair D J; Dclais, Anne-Ccile; Wilson, Timothy J; Gartner, Anton; Lilley, David M J

    2015-12-22

    We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution.The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of theDNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction. PMID:26686639

  18. Builders Challenge High Performance Builder Spotlight - NextGen Home, Las Vegas, Nevada

    SciTech Connect

    2009-01-01

    Building America Builders Challenge fact sheet on the NextGen demo home built in Las Vegas. The home has a Home Energy Rating System (HERS) index score of 44 with R-40 spray foam attic insulation, R-40 insulated concrete walls, and a 4kW DC solar laminate

  19. Introduction of Orimulsion{sup R} fuel into PowerGen PLC (UK)

    SciTech Connect

    Tombs, R.

    1995-09-01

    PowerGen has 4GW of oil fired plant comprising three power stations. Whilst burning fuel oil the load factor has been very low at between 3 and 20% because of the variable fuel price. Orimulsion, which is a bitumen-in-water emulsion, was seen as a candidate substitute fuel because of its stable cost. Because Orimulsion has very different characteristics to those of fuel oil, before committing itself to the fuel PowerGen decided to conduct full boiler trials to establish the effect of the fuel on the plant, the modifications that would be necessary to convert to full commercial operation and the environmental implications. This paper describes the outcome of the early trials that took place at each of the three power stations and the modifications that were necessary to convert plant at two of the stations. PowerGen is currently the world`s largest user of Orimulsion, consuming up to 1.5 m tonnes each year at two sites and the operational experience at each site since the start of commercial operation is summarized. Because of its unique experience with the use of Orimulsion, PowerGen can assist potential users in addressing the key conversion issues that need to be considered through consultancy services. A typical example of the issues addressed at a European utility is discussed in this paper.

  20. Balancing Formative and Summative Science Assessment Practices: Year One of the GenScope Assessment Project.

    ERIC Educational Resources Information Center

    Hickey, Daniel T.; Kruger, Ann Cale; Fredrick, Laura D.; Schafer, Nancy Jo; Kindfield, Ann C. H.

    This paper describes the GenScope Assessment Project, a project that is exploring ways of using multimedia computers to teach complex science content, refining sociocultural views of assessment and motivation, and considering different ways of reconciling the differences between these newer views and prior behavioral and cognitive views. The…

  1. GEN1 promotes Holliday junction resolution by a coordinated nick and counter-nick mechanism

    PubMed Central

    Chan, Ying Wai; West, Stephen

    2015-01-01

    Holliday junctions (HJs) that physically link sister chromatids or homologous chromosomes are formed as intermediates during DNA repair by homologous recombination. Persistent recombination intermediates are acted upon by structure-selective endonucleases that are required for proper chromosome segregation at mitosis. Here, we have purified full-length human GEN1 protein and show that it promotes Holliday junction resolution by a mechanism that is analogous to that exhibited by the prototypic HJ resolvase E. coli RuvC. We find that GEN1 cleaves HJs by a nick and counter-nick mechanism involving dual co-ordinated incisions that lead to the formation of ligatable nicked duplex products. As observed with RuvC, cleavage of the first strand is rate limiting, while second strand cleavage is rapid. In contrast to RuvC, however, GEN1 is largely monomeric in solution, but dimerizes on the HJ. Using HJs containing non-cleavable phosphorothioate-containing linkages in one strand, we show that the two incisions can be uncoupled and that the first nick occurs upon GEN1 dimerization at the junction. These results indicate that the mechanism of HJ resolution is largely conserved from bacteria to man, despite a lack of sequence homology between the resolvases. PMID:26578604

  2. pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

    PubMed Central

    Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.

    2015-01-01

    Background Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. Methods In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. Results We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/). PMID:26258475

  3. Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

    PubMed Central

    Bybee, Seth M.; Bracken-Grissom, Heather; Haynes, Benjamin D.; Hermansen, Russell A.; Byers, Robert L.; Clement, Mark J.; Udall, Joshua A.; Wilcox, Edward R.; Crandall, Keith A.

    2011-01-01

    Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach. PMID:22002916

  4. Microcetus lappus gen. nov., sp. nov.: new species of ciliated protozoon from the bovine rumen.

    PubMed Central

    Orpin, C G; Mathiesen, S D

    1986-01-01

    A new species of small, ciliated protozoon, Microcetus lappus gen. nov., sp. nov., from the rumen of Norwegian Red cattle is described. M. lappus possesses a novel cytopharyngeal apparatus of two rod-shaped structures, one situated on the dorsal side of the buccal cavity and one on the ventral side, suggesting that it belongs to a previously undescribed taxon. Images PMID:3094449

  5. Extending Validated Human Performance Models to Explore NextGen Concepts

    NASA Technical Reports Server (NTRS)

    Gore, Brian Francis; Hooey, Becky Lee; Mahlstedt, Eric; Foyle, David C.

    2012-01-01

    To meet the expected increases in air traffic demands, NASA and FAA are researching and developing Next Generation Air Transportation System (NextGen) concepts. NextGen will require substantial increases in the data available to pilots on the flight deck (e.g., weather,wake, traffic trajectory predictions, etc.) to support more precise and closely coordinated operations (e.g., self-separation, RNAV/RNP, and closely spaced parallel operations, CSPOs). These NextGen procedures and operations, along with the pilot's roles and responsibilities, must be designed with consideration of the pilot's capabilities and limitations. Failure to do so will leave the pilots, and thus the entire aviation system, vulnerable to error. A validated Man-machine Integration and design Analysis System (MIDAS) v5 model was extended to evaluate anticipated changes to flight deck and controller roles and responsibilities in NextGen approach and Land operations. Compared to conditions when the controllers are responsible for separation on decent to land phase of flight, the output from these model predictions suggest that the flight deck response time to detect the lead aircraft blunder will decrease, pilot scans to the navigation display will increase, and workload will increase.

  6. Visualizing and Sharing Results in Bioinformatics Projects: GBrowse and GenBank Exports

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Effective tools for presenting and sharing data are necessary for collaborative projects, typical for bioinformatics. In order to facilitate sharing our data with other genomics, molecular biology, and bioinformatics researchers, we have developed software to export our data to GenBank and combined ...

  7. Working with Gen Y Teachers: Dealing with a Changing Teacher Workforce

    ERIC Educational Resources Information Center

    Williamson, Ronald; Meyer-Looze, Catherine

    2010-01-01

    A significant change is coming to American classrooms. As Baby Boomer teachers retire and are replaced by members of Generation Y (born between 1977 and 1995) there is growing evidence that they come from a far different set of experiences, experiences that will shape their lives and their careers (Coggins, 2008). Members of Gen Y share several…

  8. Gen Y Recruitment: Understanding Graduate Intentions to Join an Organisation Using the Theory of Planned Behaviour

    ERIC Educational Resources Information Center

    Warmerdam, Amanda; Lewis, Ioni; Banks, Tamara

    2015-01-01

    Purpose: Using the Theory of Planned Behaviour (TPB) framework, the purpose of this paper is to explore whether the standard TPB constructs explained variance in Generation Y (Gen Y) individuals' intentions to join their ideal organisation. Design/methodology/approach: A mixed methods approach was used featuring qualitative and quantitative…

  9. CottonGen: a genomics, genetics and breeding database for cotton research

    PubMed Central

    Yu, Jing; Jung, Sook; Cheng, Chun-Huai; Ficklin, Stephen P.; Lee, Taein; Zheng, Ping; Jones, Don; Percy, Richard G.; Main, Dorrie

    2014-01-01

    CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST. PMID:24203703

  10. Revision of “Phyllobrotica” from Taiwan with description of Jolibrotica gen. n. (Coleoptera, Chrysomelidae, Galerucinae)

    PubMed Central

    Lee, Chi-Feng; Bezděk, Jan

    2015-01-01

    Abstract All Taiwanese species formerly classified the genus Phyllobrotica Chevrolat, 1836 are revised. Jolibrotica Lee & Bezděk, gen. n., is described for Phyllobrotica sauteri (Chûjô, 1935) (Taiwan, China: Guangxi) and Phyllobrotica chujoi Kimoto, 1969 (Taiwan). Phyllobrotica shirozui Kimoto, 1969 is transferred to the genus Haplosomoides. All species are redescribed and their diagnostic characters illustrated. PMID:26798315

  11. Plant MetGenMAP: an integrative analysis system for plant systems biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. P...

  12. GWAS in a Box: Statistical and Visual Analytics of Structured Associations via GenAMap

    PubMed Central

    Xing, Eric P.; Curtis, Ross E.; Schoenherr, Georg; Lee, Seunghak; Yin, Junming; Puniyani, Kriti; Wu, Wei; Kinnaird, Peter

    2014-01-01

    With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. PMID:24905018

  13. Gen Y Recruitment: Understanding Graduate Intentions to Join an Organisation Using the Theory of Planned Behaviour

    ERIC Educational Resources Information Center

    Warmerdam, Amanda; Lewis, Ioni; Banks, Tamara

    2015-01-01

    Purpose: Using the Theory of Planned Behaviour (TPB) framework, the purpose of this paper is to explore whether the standard TPB constructs explained variance in Generation Y (Gen Y) individuals' intentions to join their ideal organisation. Design/methodology/approach: A mixed methods approach was used featuring qualitative and quantitative

  14. POWER-GEN `96 international. Book V - D. Operating plants. Volume 13-15

    SciTech Connect

    1996-12-31

    This is the fifth book in a six book set for the Power-Gen 96 International Conference and Exhibition. This book contains Volumes 13 through 15. Topics covered by volumes 13 through 15 include: performance enhancement, and operations & management. Subtopics include: hydro and cogeneration, particulate control systems, turbines, boilers, power plant chemistry, and preventive and predictive maintenance.

  15. Overview of NASA's Next Generation Air Transportation System (NextGen) Research

    NASA Technical Reports Server (NTRS)

    Swenson, Harry N.

    2009-01-01

    This slide presentation is an overview of the research for the Next Generation Air Transportation System (NextGen). Included is a review of the current air transportation system and the challenges of air transportation research. Also included is a review of the current research highlights and significant accomplishments.

  16. The GenTechnique Project: Developing an Open Environment for Learning Molecular Genetics.

    ERIC Educational Resources Information Center

    Calza, R. E.; Meade, J. T.

    1998-01-01

    The GenTechnique project at Washington State University uses a networked learning environment for molecular genetics learning. The project is developing courseware featuring animation, hyper-link controls, and interactive self-assessment exercises focusing on fundamental concepts. The first pilot course featured a Web-based module on DNA

  17. Environmental Information for the U.S. Next Generation Air Transportation System (NextGen)

    NASA Astrophysics Data System (ADS)

    Murray, J.; Miner, C.; Pace, D.; Minnis, P.; Mecikalski, J.; Feltz, W.; Johnson, D.; Iskendarian, H.; Haynes, J.

    2009-09-01

    It is estimated that weather is responsible for approximately 70% of all air traffic delays and cancellations in the United States. Annually, this produces an overall economic loss of nearly 40B. The FAA and NASA have determined that weather impacts and other environmental constraints on the U.S. National Airspace System (NAS) will increase to the point of system unsustainability unless the NAS is radically transformed. A Next Generation Air Transportation System (NextGen) is planned to accommodate the anticipated demand for increased system capacity and the super-density operations that this transformation will entail. The heart of the environmental information component that is being developed for NextGen will be a 4-dimensional data cube which will include a single authoritative source comprising probabilistic weather information for NextGen Air Traffic Management (ATM) systems. Aviation weather constraints and safety hazards typically comprise meso-scale, storm-scale and microscale observables that can significantly impact both terminal and enroute aviation operations. With these operational impacts in mind, functional and performance requirements for the NextGen weather system were established which require significant improvements in observation and forecasting capabilities. This will include satellite observations from geostationary and/or polar-orbiting hyperspectral sounders, multi-spectral imagers, lightning mappers, space weather monitors and other environmental observing systems. It will also require improved in situ and remotely sensed observations from ground-based and airborne systems. These observations will be used to better understand and to develop forecasting applications for convective weather, in-flight icing, turbulence, ceilings and visibility, volcanic ash, space weather and the environmental impacts of aviation. Cutting-edge collaborative research efforts and results from NASA, NOAA and the FAA which address these phenomena are summarized. In 2003, a Joint Planning and Development Office (JPDO) was established by public law to meet the significant challenges that NextGen presents. JPDO partners were chartered which include, but are not limited to, the Federal Aviation Administration (FAA), the National Oceanic and Atmospheric Administration (NOAA), the National Aeronautics and Space Administration (NASA), the Department of Defense (DOD) and broad elements of academia and the aviation industry. This paper provides the aviation meteorology community with useful insight on salient NextGen environmental information requirements that have been developed by the JPDO Weather Working Group's Environmental Information Team. These efforts will help to define observation and forecast systems needed to support NextGen and to develop the operational applications for NextGen aviation weather information. Another major goal of this paper is to inform the international weather community of our research progress and plans for NextGen, to foster research collaboration with our colleagues, and to exchange information to maximize success of NextGen, SESAR and related initiatives world-wide.

  18. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework.

    PubMed

    Parks, Donovan H; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S; Armanini, David G; Baird, Donald J; Langille, Morgan G I; Beiko, Robert G

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  19. GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework

    PubMed Central

    Parks, Donovan H.; Mankowski, Timothy; Zangooei, Somayyeh; Porter, Michael S.; Armanini, David G.; Baird, Donald J.; Langille, Morgan G. I.; Beiko, Robert G.

    2013-01-01

    GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis. PMID:23922841

  20. Transduction of Photoreceptors With Equine Infectious Anemia Virus Lentiviral Vectors: Safety and Biodistribution of StarGen for Stargardt Disease

    PubMed Central

    Binley, Katie; Widdowson, Peter; Loader, Julie; Kelleher, Michelle; Iqball, Sharifah; Ferrige, Georgina; de Belin, Jackie; Carlucci, Marie; Angell-Manning, Diana; Hurst, Felicity; Ellis, Scott; Miskin, James; Fernandes, Alcides; Wong, Paul; Allikmets, Rando; Bergstrom, Christopher; Aaberg, Thomas; Yan, Jiong; Kong, Jian; Gouras, Peter; Prefontaine, Annick; Vezina, Mark; Bussieres, Martin; Naylor, Stuart; Mitrophanous, Kyriacos A.

    2013-01-01

    Purpose. StarGen is an equine infectious anemia virus (EIAV)-based lentiviral vector that expresses the photoreceptor-specific adenosine triphosphate (ATP)-binding cassette transporter (ABCA4) protein that is mutated in Stargardt disease (STGD1), a juvenile macular dystrophy. EIAV vectors are able to efficiently transduce rod and cone photoreceptors in addition to retinal pigment epithelium in the adult macaque and rabbit retina following subretinal delivery. The safety and biodistribution of StarGen following subretinal delivery in macaques and rabbits was assessed. Methods. Regular ophthalmic examinations, IOP measurements, ERG responses, and histopathology were carried out in both species to compare control and vector-treated eyes. Tissue and fluid samples were obtained to evaluate the persistence, biodistribution, and shedding of the vector following subretinal delivery. Results. Ophthalmic examinations revealed a slightly higher level of inflammation in StarGen compared with control treated eyes in both species. However, inflammation was transient and no overt toxicity was observed in StarGen treated eyes and there were no abnormal clinical findings. There was no StarGen-associated rise in IOP or abnormal ERG response in either rabbits or macaques. Histopathologic examination of the eyes did not reveal any detrimental changes resulting from subretinal administration of StarGen. Although antibodies to StarGen vector components were detected in rabbit but not macaque serum, this immunologic response did not result in any long-term toxicity. Biodistribution analysis demonstrated that the StarGen vector was restricted to the ocular compartment. Conclusions. In summary, these studies demonstrate StarGen to be well tolerated and localized following subretinal administration. PMID:23620430

  1. Generation and selection of novel estrogen receptor ligands using the de novo structure-based design tool, SkelGen.

    PubMed

    Firth-Clark, Stuart; Willems, Henritte M G; Williams, Anthony; Harris, William

    2006-01-01

    A de novo design approach to generating novel estrogen receptor (ER) ligands is described. The SkelGen program was used to generate ligands in the active sites of seven crystal structures of ERalpha. Seventeen high-scoring, diverse structures were selected from the SkelGen output and synthesized without introducing any modifications to the structures. Five ligands, four of which are novel, showed < or = 25 microM affinity, with the best compound displaying an IC50 of 340 nM. SkelGen can, therefore, be a powerful tool for designing active molecules. PMID:16562994

  2. Transfer of Pseudomonas flectens Johnson 1956 to Phaseolibacter gen. nov., in the family Enterobacteriaceae, as Phaseolibacter flectens gen. nov., comb. nov.

    PubMed

    Halpern, Malka; Fridman, Svetlana; Aizenberg-Gershtein, Yana; Izhaki, Ido

    2013-01-01

    Pseudomonas flectens Johnson 1956, a plant-pathogenic bacterium on the pods of the French bean, is no longer considered to be a member of the genus Pseudomonas sensu stricto. A polyphasic approach that included examination of phenotypic properties and phylogenetic analyses based on 16S rRNA, rpoB and atpD gene sequences supported the transfer of Pseudomonas flectens Johnson 1956 to a new genus in the family Enterobacteriaceae as Phaseolibacter flectens gen. nov., comb. nov. Two strains of Phaseolibacter flectens were studied (ATCC 12775(T) and LMG 2186); the strains shared 99.8 % sequence similarity in their 16S rRNA genes and the housekeeping gene sequences were identical. Strains of Phaseolibacter flectens shared 96.6 % or less 16S rRNA gene sequence similarity with members of different genera in the family Enterobacteriaceae and only 84.7 % sequence similarity with Pseudomonas aeruginosa LMG 1242(T), demonstrating that they are not related to the genus Pseudomonas. As Phaseolibacter flectens formed an independent phyletic lineage in all of the phylogenetic analyses, it could not be affiliated to any of the recognized genera within the family Enterobacteriaceae and therefore was assigned to a new genus. Cells were Gram-negative, straight rods, motile by means of one or two polar flagella, fermentative, facultative anaerobes, oxidase-negative and catalase-positive. Growth occurred in the presence of 0-60 % sucrose. The DNA G+C content of the type strain was 44.3 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, Pseudomonas flectens Johnson 1956 is transferred to the novel genus Phaseolibacter gen. nov. as Phaseolibacter flectens gen. nov., comb. nov. The type strain of Phaseolibacter flectens is ATCC 12775(T) = CFBP 3281(T) = ICMP 745(T) = LMG 2187(T) = NCPPB 539(T). PMID:22407791

  3. 78 FR 56263 - HydroGen Corp., QueryObject Systems Corp., Security Intelligence Technologies, Inc., Skins, Inc...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-12

    ... From the Federal Register Online via the Government Publishing Office SECURITIES AND EXCHANGE COMMISSION HydroGen Corp., QueryObject Systems Corp., Security Intelligence Technologies, Inc., Skins, Inc... and accurate information concerning the securities of Security Intelligence Technologies, Inc....

  4. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    SciTech Connect

    Sexton, David

    2012-06-01

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  5. Squamasnema amazonica n. gen. n. sp. (Heligmonellinae): A new parasite of Proechimys roberti (Rodentia: Echimyidae) in the Brazilian Amazon.

    PubMed

    Cordeiro, Helrik da Costa; Melo, Francisco Tiago de Vasconcelos; Furtado, Adriano Penha; Giese, Elane Guerreiro; Maldonado, Arnaldo; dos Santos, Jeannie Nascimento

    2015-08-01

    A new species of nematode, Squamasnema amazonica n. gen. n. sp., is described based on specimens found parasitizing the small intestine of Proechimys roberti (Rodentia: Echimyidae) collected during a survey of the fauna of Tapirap-Aquir National Forest (Brazil, Eastern Brazilian Amazon). The nematodes were fixed and processed for light microscopy and scanning electron microscopy (SEM). These nematodes were classified under the family Heligmonellidae and the subfamily Heligmonellinae. Although several species in the family Heligmonellidae exhibit discontinuous ridges, Squamasnema n. gen. and Trichotravassosia are the only genera with columns of scales along their entire body, as an apomorphy of the synlophe. Squamasnema n. gen. has columns of cuticular cells along its body, except for on the left flank, and exhibits a synlophe with no size gradient or inclination and does not present chitinized structures supporting the synlophe. Therefore, due to these morphological differences of Squamasnema n. gen., the creation of a new genus was necessary. PMID:25910627

  6. A New Genus Bifidunguiglenea gen. nov. Is Erected for the Species Glenea gestroi Gahan (Cerambycidae: Lamiinae: Saperdini)

    PubMed Central

    Lin, Mei-Ying; Tavakilian, Grard Luc

    2012-01-01

    Bifidunguiglenea gen. nov. is erected for the species Glenea gestroi Gahan, 1894. Bifidunguiglenea gestroi (Gahan, 1894) comb. nov. is redescribed. The genitalia descriptions are reported for the first time and it is newly recorded from Thailand. PMID:22815810

  7. Mercury: Next-gen Data Analysis and Annotation Pipeline (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema

    Sexton, David [Baylor

    2013-01-25

    David Sexton (Baylor) gives a talk titled "Mercury: Next-gen Data Analysis and Annotation Pipeline" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  8. Identification and Characterization of Key Human Performance Issues and Research in the Next Generation Air Transportation System (NextGen)

    NASA Technical Reports Server (NTRS)

    Lee, Paul U.; Sheridan, Tom; Poage, james L.; Martin, Lynne Hazel; Jobe, Kimberly K.

    2010-01-01

    This report identifies key human-performance-related issues associated with Next Generation Air Transportation System (NextGen) research in the NASA NextGen-Airspace Project. Four Research Focus Areas (RFAs) in the NextGen-Airspace Project - namely Separation Assurance (SA), Airspace Super Density Operations (ASDO), Traffic Flow Management (TFM), and Dynamic Airspace Configuration (DAC) - were examined closely. In the course of the research, it was determined that the identified human performance issues needed to be analyzed in the context of NextGen operations rather than through basic human factors research. The main gaps in human factors research in NextGen were found in the need for accurate identification of key human-systems related issues within the context of specific NextGen concepts and better design of the operational requirements for those concepts. By focusing on human-system related issues for individual concepts, key human performance issues for the four RFAs were identified and described in this report. In addition, mixed equipage airspace with components of two RFAs were characterized to illustrate potential human performance issues that arise from the integration of multiple concepts.

  9. Revision of J3Gen and Validity of the Attacks by Peinado et al.

    PubMed

    Peinado, Alberto; Munilla, Jorge; Fster-Sabater, Amparo

    2015-01-01

    This letter is the reply to: Remarks on Peinado et al.'s Analysis of J3Gen by J. Garcia-Alfaro, J. Herrera-Joancomart and J. Meli-Segu published in Sensors 2015, 15, 6217-6220. Peinado et al. cryptanalyzed the pseudorandom number generator proposed by Meli-Segu et al., describing two possible attacks. Later, Garcia-Alfaro claimed that one of this attack did not hold in practice because the assumptions made by Peinado et al. were not correct. This letter reviews those remarks, showing that J3Gen is anyway flawed and that, without further information, the interpretation made by Peinado et al. seems to be correct. PMID:26007740

  10. Hanford Meteorological Station computer codes: Volume 1, The GEN computer code

    SciTech Connect

    Buck, J.W.; Andrews, G.L.

    1987-07-01

    The Hanford Meteorological Station, operated by Pacific Northwest Laboratory, issues general weather forecasts twice a day. The GEN computer code is used to archive the 24-hour forecasts and apply quality assurance checks to the forecast data. This code accesses an input file, which contains the date and hour of the previous forecast, and an output file, which contains 24-hour forecasts for the current month. As part of the program, a data entry form consisting of 14 fields that describe various weather conditions must be filled in. The information on the form is appended to the current 24-hour monthly forecast file, which provides an archive for the 24-hour general weather forecasts. This report consists of several volumes documenting the various computer codes used at the Hanford Meteorological Station. This volume describes the implementation and operation of the GEN computer code at the station.

  11. Towards Structuring Unstructured GenBank Metadata for Enhancing Comparative Biological Studies

    PubMed Central

    Chen, Elizabeth S.; Sarkar, Indra Neil

    2011-01-01

    Within large sequence repositories such as GenBank there is a wealth of metadata providing contextual information that may enhance search and retrieval of relevant sequences for a range of subsequent analyses. One challenge is the use of free-text in these metadata fields where approaches are needed to extract, structure, and encode essential information. The goal of the present study was to explore the feasibility of using a combination of existing resources for annotating unstructured GenBank metadata, initially focusing on the host and isolation_source fields. This paper summarizes early results for 10 host organisms that include a characterization of associated isolation sources with respect to biomedical ontologies and semantic types. The findings from this preliminary study provide insights to the rich amount of information captured within these unstructured metadata, guidance for addressing the challenges and issues encountered, and highlight the potential value for enriching comparative biological studies towards improving human health. PMID:22211174

  12. Gen 2.0 Mixer/Ejector Nozzle Test at LSAF June 1995 to July 1996

    NASA Technical Reports Server (NTRS)

    Arney, L. D.; Sandquist, D. L.; Forsyth, D. W.; Lidstone, G. L.; Long-Davis, Mary Jo (Technical Monitor)

    2005-01-01

    Testing of the HSCT Generation 2.0 nozzle model hardware was conducted at the Boeing Low Speed Aeroacoustic Facility, LSAF. Concurrent measurements of noise and thrust were made at critical takeoff design conditions for a variety of mixer/ejector model hardware. Design variables such as suppressor area ratio, mixer area ratio, liner type and thickness, ejector length, lobe penetration, and mixer chute shape were tested. Parallel testing was conducted at G.E.'s Cell 41 acoustic free jet facility to augment the LSAF test. The results from the Gen 2.0 testing are being used to help shape the current nozzle baseline configuration and guide the efforts in the upcoming Generation 2.5 and 3.0 nozzle tests. The Gen 2.0 results have been included in the total airplane system studies conducted at MDC and Boeing to provide updated noise and thrust performance estimates.

  13. A REVIEW PAPER ON AGING EFFECTS IN ALLOY 617 FOR GEN IVNUCLEAR REACTOR APPLICATIONS

    SciTech Connect

    Ren, Weiju; Swindeman, Robert W

    2009-01-01

    To understand the response of Alloy 617 to long-time exposure conditions and determine the supplementary data needs for structural components in Gen IV nuclear reactors, the literature of aging and aging effects in the alloy was reviewed. Most of the reviewed data were produced in connection with the international research effort supporting High Temperature Gas-Cooled Reactor (HTGR) projects in the 1970s and 1980s. Topics considered included microstructural changes, hardness, tensile properties, toughness, creep-rupture, fatigue, and crack growth. It became clear that, for the long-time, very high temperature conditions of the Gen IV reactors, a significant effort would be needed to fully understand and characterize property changes. Several topics for further research were recommended.

  14. A REVIEW OF AGING EFFECTS IN ALLOY 617 FOR GEN IV NUCLEAR REACTOR APPLICATIONS

    SciTech Connect

    Ren, Weiju; Swindeman, Robert W

    2006-01-01

    The literature was reviewed of aging and aging effects in Alloy 617 to determine the supplementary data needed to understand the response of the alloy to long-time exposure conditions being considered for structural components in Gen IV nuclear reactors. Most of the data were produced in connection with the international research effort supporting High Temperature Gas-Cooled Reactor (HTGR) projects in the 1970s and 1980s. Topics considered included microstructural changes, hardness, tensile properties, toughness, creep-rupture, fatigue, and crack growth. It became clear that, for the long-time, very high temperature conditions of the Gen IV reactors, a significant effort would be needed to fully understand and characterize property changes. Several topics for further research were recommended.

  15. Developing a Nuclear Grade of Alloy 617 for Gen IV Nuclear Energy Systems

    SciTech Connect

    Ren, Weiju; Swindeman, Robert W; Santella, Michael L

    2010-01-01

    Alloy 617, an attractive material not particularly developed for nuclear use, is now being considered as a leading candidate alloy by several countries for applications in the Gen IV Nuclear Energy Systems. An extensive review of its existing data suggests that it would be beneficial to refine the alloy s specification to a nuclear grade for the intended Gen IV systems. In this paper, rationale for developing a nuclear grade of the alloy is first discussed through an analysis on existing data from various countries. Then initial experiments for refining the alloy specification are described. Preliminary results have suggested the feasibility of the refinement approach, as well as the possibility for achieving a desirable nuclear grade. Based on the results, further research activities are recommended.

  16. Neutron Arm Study and Calibration for the GEn Experiment at Thomas Jefferson National Laboratory

    SciTech Connect

    Timothy Ngo

    2007-07-01

    The measurement of the neutron electric form factor, GEn, will allow us to solve indirectly for the quark charge distribution inside of the neutron. With the equipment at Jefferson Lab we have measured GEn at four momentum transfer values of Q**2 at 1.3, 2.4 and 3.4 (GeV/c)**2 using a polarized electron beam and polarized Helium target. The scattered electrons off of the Helium target are detected in the BigBite spectrometer and the recoiling neutrons from the Helium are detected in the Neutron Arm, which is composed of an array of scintillators. The main focus of this thesis will be devoted to the geometry, timing and energy calibrations of the Neutron Arm.

  17. Parametric Modeling of the Safety Effects of NextGen Terminal Maneuvering Area Conflict Scenarios

    NASA Technical Reports Server (NTRS)

    Rogers, William H.; Waldron, Timothy P.; Stroiney, Steven R.

    2011-01-01

    The goal of this work was to analytically identify and quantify the issues, challenges, technical hurdles, and pilot-vehicle interface issues associated with conflict detection and resolution (CD&R)in emerging operational concepts for a NextGen terminal aneuvering area, including surface operations. To this end, the work entailed analytical and trade studies focused on modeling the achievable safety benefits of different CD&R strategies and concepts in the current and future airport environment. In addition, crew-vehicle interface and pilot performance enhancements and potential issues were analyzed based on review of envisioned NextGen operations, expected equipage advances, and human factors expertise. The results of perturbation analysis, which quantify the high-level performance impact of changes to key parameters such as median response time and surveillance position error, show that the analytical model developed could be useful in making technology investment decisions.

  18. Description of Distorhabditis poonchiana n. gen., n. sp. (Nematoda: Rhabditidae) from Jammu and Kashmir, India

    PubMed Central

    Shah, Ali Asghar; Vaid, Shavish; Hussain, Abid; Ahmad, Rakeeb

    2015-01-01

    Distorhabditis poonchiana n. gen., n. sp. from humus in Jammu and Kashmir, India, is described and illustrated. The new genus is characterized by a small body; slightly setoff labial region; long tubular gymnostom; prominently cuticularized cheilostom; absence of glottoid apparatus; monoprodelphic reproductive system; vulva (V) = 81 to 84; spicules with trifurcated distal ends, simple gubernaculum, peloderan bursa with eight pairs of bursal papillae arranged in 1 + 1 + 1 + 2 + 1 + 2 arrangement. PMID:26941466

  19. Dual-track CCS stakeholder engagement: Lessons learned from FutureGen in Illinois

    USGS Publications Warehouse

    Hund, G.; Greenberg, S.E.

    2011-01-01

    FutureGen, as originally planned, was to be the world's first coal-fueled, near-zero emissions power plant with fully integrated, 90% carbon capture and storage (CCS). From conception through siting and design, it enjoyed strong support from multiple stakeholder groups, which benefited the overall project. Understanding the stakeholder engagement process for this project provides valuable insights into the design of stakeholder programs for future CCS projects. FutureGen is one of few projects worldwide that used open competition for siting both the power plant and storage reservoir. Most site proposals were coordinated by State governments. It was unique in this and other respects relative to the site selection method used on other DOE-supported projects. At the time of site selection, FutureGen was the largest proposed facility designed to combine an integrated gasification combined cycle (IGCC) coal-fueled power plant with a CCS system. Stakeholder engagement by states and the industry consortium responsible for siting, designing, building, and operating the facility took place simultaneously and on parallel tracks. On one track were states spearheading state-wide site assessments to identify candidate sites that they wanted to propose for consideration. On the other track was a public-private partnership between an industry consortium of thirteen coal companies and electric utilities that comprised the FutureGen Alliance (Alliance) and the U.S. Department of Energy (DOE). The partnership was based on a cooperative agreement signed by both parties, which assigned the lead for siting to the Alliance. This paper describes the stakeholder engagement strategies used on both of these tracks and provides examples from the engagement process using the Illinois semi-finalist sites. ?? 2011 Published by Elsevier Ltd.

  20. Yamaguchia toyensis n. sp., n. gen. (Annelida, Clitellata, Lumbriculidae) from profundal lake habitat in Japan

    USGS Publications Warehouse

    Fend, S.V.; Ohtaka, A.

    2004-01-01

    Yamaguchia toyensis n. sp., n. gen. is described from an oligotrophic caldera lake, Lake Toya, Hokkaido, Japan. Although the taxonomic affinities are unknown, the genus differs from all other Lumbriculidae in having the combination of testes and atria in X, a single, prosoporous male funnel per atrium, and spermathecae in XI. Unlike other Japanese lakes that have thus far been surveyed, Lake Toya supports abundant populations of lumbriculids in the profundal benthos.

  1. Generalized background error covariance matrix model (GEN_BE v2.0)

    NASA Astrophysics Data System (ADS)

    Descombes, G.; Aulign, T.; Vandenberghe, F.; Barker, D. M.; Barr, J.

    2015-03-01

    The specification of state background error statistics is a key component of data assimilation since it affects the impact observations will have on the analysis. In the variational data assimilation approach, applied in geophysical sciences, the dimensions of the background error covariance matrix (B) are usually too large to be explicitly determined and B needs to be modeled. Recent efforts to include new variables in the analysis such as cloud parameters and chemical species have required the development of the code to GENerate the Background Errors (GEN_BE) version 2.0 for the Weather Research and Forecasting (WRF) community model. GEN_BE allows for a simpler, flexible, robust, and community-oriented framework that gathers methods used by some meteorological operational centers and researchers. We present the advantages of this new design for the data assimilation community by performing benchmarks of different modeling of B and showing some of the new features in data assimilation test cases. As data assimilation for clouds remains a challenge, we present a multivariate approach that includes hydrometeors in the control variables and new correlated errors. In addition, the GEN_BE v2.0 code is employed to diagnose error parameter statistics for chemical species, which shows that it is a tool flexible enough to implement new control variables. While the generation of the background errors statistics code was first developed for atmospheric research, the new version (GEN_BE v2.0) can be easily applied to other domains of science and chosen to diagnose and model B. Initially developed for variational data assimilation, the model of the B matrix may be useful for variational ensemble hybrid methods as well.

  2. La Carte du Ciel : genèse, déroulement et issue

    NASA Astrophysics Data System (ADS)

    Chinnici, I.

    2008-06-01

    Ce chapitre propose une vue panoramique de la Carte du Ciel en détaillant sa genèse, son déroulement et son issue en insistant sur les objectifs scientifiques initiaux et leur évolution au cours du temps. Les aspects politiques de l'entreprise sont également analysés ; ils permettent de souligner les enjeux nationaux et internationaux qui sous-tendent le projet.

  3. GEN IV MATERIALS HANDBOOK BETA RELEASE FOR STRUCTURAL AND FUNCTIONAL EVALUATION

    SciTech Connect

    Ren, Weiju; Luttrell, Claire

    2006-09-12

    Development of the Gen IV Materials Handbook is briefly summarized up to date. Current status of the Handbook website construction is described. The developed Handbook components and access control of the beta version are discussed for the present evaluation release. Detailed instructions and examples are given to provide guidance for evaluators to browse the constructed parts and use all the currently developed functionalities of the Handbook in evaluation.

  4. Complexity analysis of the Next Gen Air Traffic Management System: trajectory based operations.

    PubMed

    Lyons, Rhonda

    2012-01-01

    According to Federal Aviation Administration traffic predictions currently our Air Traffic Management (ATM) system is operating at 150 percent capacity; forecasting that within the next two decades, the traffic with increase to a staggering 250 percent [17]. This will require a major redesign of our system. Today's ATM system is complex. It is designed to safely, economically, and efficiently provide air traffic services through the cost-effective provision of facilities and seamless services in collaboration with multiple agents however, contrary the vision, the system is loosely integrated and is suffering tremendously from antiquated equipment and saturated airways. The new Next Generation (Next Gen) ATM system is designed to transform the current system into an agile, robust and responsive set of operations that are designed to safely manage the growing needs of the projected increasingly complex, diverse set of air transportation system users and massive projected worldwide traffic rates. This new revolutionary technology-centric system is dynamically complex and is much more sophisticated than it's soon to be predecessor. ATM system failures could yield large scale catastrophic consequences as it is a safety critical system. This work will attempt to describe complexity and the complex nature of the NextGen ATM system and Trajectory Based Operational. Complex human factors interactions within Next Gen will be analyzed using a proposed dual experimental approach designed to identify hazards, gaps and elicit emergent hazards that would not be visible if conducted in isolation. Suggestions will be made along with a proposal for future human factors research in the TBO safety critical Next Gen environment. PMID:22317416

  5. Erection of a new genus Biura gen. nov., of the subtribe Aolina (Hemiptera: Cicadidae: Cicadinae: Dundubiini).

    PubMed

    Lee, Young June; Sanborn, Allen F

    2015-01-01

    A new genus, Biura gen. nov., is erected within the subtribe Aolina Boulard, 2012, designating Haphsa bicolora Sanborn, 2009 as the type species. This new genus is distinguished from all other genera in Aolina by the light-colored body lacking prominent markings, non-infuscated wings, very small and short male operculum, thin and long uncal lobes, and distinctly prominent basal lobes of the pygofer. PMID:26624729

  6. Geochemical Monitoring Considerations for the FutureGen 2.0 Project

    DOE PAGESBeta

    Amonette, James E.; Johnson, Timothy A.; Spencer, Clayton F.; Zhong, Lirong; Szecsody, James E.; Vermeul, Vince R.

    2014-12-31

    Geochemical monitoring is an essential component of a suite of monitoring technologies designed to evaluate CO2 mass balance and detect possible loss of containment at the FutureGen 2.0 geologic sequestration site near Jacksonville, IL. This presentation gives an overview of the potential geochemical approaches and tracer technologies that were considered, and describes the evaluation process by which the most cost-effective and robust of these were selected for implementation

  7. Development of an Enhanced GenVARR™ (Generator Volt Ampere Reactive Reserve) System

    SciTech Connect

    Schatz, Joe E.

    2009-03-12

    Transmission system operators require near real time knowledge of reactive power capability to reliably operate large electric power transmission systems. Reactive power produced by, or capable of being produced by, a power generator is often estimated based on a series of mega volt amperes (MVA) capability curves for the generator. These curves indicate the ability of the generator to produce real and reactive power under a variety of conditions. In transmission planning and operating studies, it is often assumed, based on estimates for these capability curves, that the generator can provide its rated MVA capability output when needed for system stability However, generators may not always operate at levels depicted by the maximum MVA capability curve due to present constraints. Transmission system operators utilizing the generators’ capability curves for operation decisions regarding transmission system stability or for planning horizons may overestimate the capability of the generators to supply reactive power when required. Southern Company has enhanced GenVARR(TM), the system of plant data query, retrieval, and analysis and calculates the actual – not estimated -- remaining reactive power output capability. The remaining reactive output is considered spinning reserve and is displayed graphically to transmission control center and generating plant operators to identify real time VAR limits. GenVARR is capable of aggregating generators from a defined region, or other user selectable combinations, to represent the available reserves that the operators are specifically interested in. GenVARR(TM) has been put into live production operation and is expected to significantly improve the overall visibility of the reactive reserve capability of the system. This new version of GenVARR(TM) significantly enhances the products structure and performance, and enables links to other key transmission system operation tools.

  8. MicroGen: a MIAME compliant web system for microarray experiment information and workflow management

    PubMed Central

    Burgarella, Sarah; Cattaneo, Dario; Pinciroli, Francesco; Masseroli, Marco

    2005-01-01

    Background Improvements of bio-nano-technologies and biomolecular techniques have led to increasing production of high-throughput experimental data. Spotted cDNA microarray is one of the most diffuse technologies, used in single research laboratories and in biotechnology service facilities. Although they are routinely performed, spotted microarray experiments are complex procedures entailing several experimental steps and actors with different technical skills and roles. During an experiment, involved actors, who can also be located in a distance, need to access and share specific experiment information according to their roles. Furthermore, complete information describing all experimental steps must be orderly collected to allow subsequent correct interpretation of experimental results. Results We developed MicroGen, a web system for managing information and workflow in the production pipeline of spotted microarray experiments. It is constituted of a core multi-database system able to store all data completely characterizing different spotted microarray experiments according to the Minimum Information About Microarray Experiments (MIAME) standard, and of an intuitive and user-friendly web interface able to support the collaborative work required among multidisciplinary actors and roles involved in spotted microarray experiment production. MicroGen supports six types of user roles: the researcher who designs and requests the experiment, the spotting operator, the hybridisation operator, the image processing operator, the system administrator, and the generic public user who can access the unrestricted part of the system to get information about MicroGen services. Conclusion MicroGen represents a MIAME compliant information system that enables managing workflow and supporting collaborative work in spotted microarray experiment production. PMID:16351755

  9. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

    PubMed Central

    Breider, Sven; Scheuner, Carmen; Schumann, Peter; Fiebig, Anne; Petersen, Jörn; Pradella, Silke; Klenk, Hans-Peter; Brinkhoff, Thorsten; Göker, Markus

    2014-01-01

    Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended. PMID:25157246

  10. Two New Freshwater Woloszynskioids Asulcocephalium miricentonis gen. et sp. nov. and Leiocephalium pseudosanguineum gen. et sp. nov. (Suessiaceae, Dinophyceae) Lacking an Apical Furrow Apparatus.

    PubMed

    Takahashi, Kazuya; Moestrup, jvind; Jordan, Richard W; Iwataki, Mitsunori

    2015-12-01

    Two new woloszynskioid dinoflagellates, Asulcocephalium miricentonis gen. et sp. nov. and Leiocephalium pseudosanguineum gen. et sp. nov., are described from Japanese freshwater ponds on the basis of bright field and fluorescence light microscopy, scanning and transmission electron microscopy, and molecular phylogeny inferred from rDNA sequences. Asulcocephalium miricentonis has a spherical anterior nucleus and chloroplast with a pyrenoid penetrated by the cytoplasm. This species has 9-12 latitudinal series of amphiesmal vesicles (AVs), including an apparently large AV on the right ventral side of the epicone. Leiocephalium pseudosanguineum has a U-shaped nucleus in the epicone and chloroplasts without a pyrenoid. This species has at least 24 latitudinal series of AVs. The characteristic features of both species were brick-like material (type E) in the eyespot and the lack of an apical furrow. These features coincide with those of Polarella glacialis, but the two species differ in cell shape, number and arrangement of AVs, shape of resting cysts, and habitats; i.e., P. glacialis has been reported only from marine cold waters. Molecular phylogeny revealed that A. miricentonis and L. pseudosanguineum were positioned in the Suessiaceae and closely related to Piscinoodinium sp., but their relationship to Polarella and other reported taxa was not supported. PMID:26599726

  11. Taxonomy of the Proisotoma complex. V. Sexually dimorphic Ephemerotoma gen. nov. (Collembola: Isotomidae).

    PubMed

    Potapov, Mikhail; Kahrarian, Morteza; Deharveng, Louis; Shayanmehr, Masoumeh

    2015-01-01

    A new genus is proposed based on a new species from Iran, Ephemerotoma skarzynskii gen. et sp. nov., and three known species: E. huadongensis (Chen, 1985) comb. nov., E. multituberculata (Martynova, 1971) comb. nov. and E. porcella (Ellis, 1976) comb. nov. The genus shares the characters of Subisotoma Stach and Proctostephanus Börner and is distributed in southern areas of Eurasia (Eastern Mediterranean, Iran, Tajikistan, China). Ephemerotoma gen. nov. belongs to the Proisotoma-complex and is characterized by a simple maxillary palp, only 4 guards on labial papilla E and 2 prelabral chaetae. Four s-chaetae on Abd.V are arranged in two rows, two anterior and two posterior chaetae. All members of Ephemerotoma gen. nov. are redescribed or discussed based on type or fresh material, and a key to species of the genus is given. Scutisotoma potapovi Xie & Chen, 2008 is considered a synonym of E. huadongensis, while Proisotoma anopolitana is moved to the genus Proctostephanus. Sexual dimorphism is described for three species. PMID:26701434

  12. Structures and stability of metal-doped GenM (n = 9, 10) clusters

    NASA Astrophysics Data System (ADS)

    Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

    2015-06-01

    The lowest-energy structures of neutral and cationic GenM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Such cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.

  13. GenColors-based comparative genome databases for small eukaryotic genomes

    PubMed Central

    Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Shnel, Jrgen; Glckner, Gernot

    2013-01-01

    Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources. PMID:23193285

  14. Enhanced and Synthetic Vision for Terminal Maneuvering Area NextGen Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

    2011-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  15. CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases

    PubMed Central

    V, Alexandar; Nayar, Pradeep G.; Murugesan, R.; Mary, Beaulah; P, Darshana; Ahmed, Shiek S. S. J.

    2015-01-01

    Cardiovascular diseases (CVDs) account for high morbidity and mortality worldwide. Both, genetic and epigenetic factors are involved in the enumeration of various cardiovascular diseases. In recent years, a vast amount of multi-omics data are accumulated in the field of cardiovascular research, yet the understanding of key mechanistic aspects of CVDs remain uncovered. Hence, a comprehensive online resource tool is required to comprehend previous research findings and to draw novel methodology for understanding disease pathophysiology. Here, we have developed a literature-based database, CardioGenBase, collecting gene-disease association from Pubmed and MEDLINE. The database covers major cardiovascular diseases such as cerebrovascular disease, coronary artery disease (CAD), hypertensive heart disease, inflammatory heart disease, ischemic heart disease and rheumatic heart disease. It contains ~1,500 cardiovascular disease genes from ~2,4000 research articles. For each gene, literature evidence, ontology, pathways, single nucleotide polymorphism, protein-protein interaction network, normal gene expression, protein expressions in various body fluids and tissues are provided. In addition, tools like gene-disease association finder and gene expression finder are made available for the users with figures, tables, maps and venn diagram to fit their needs. To our knowledge, CardioGenBase is the only database to provide gene-disease association for above mentioned major cardiovascular diseases in a single portal. CardioGenBase is a vital online resource to support genome-wide analysis, genetic, epigenetic and pharmacological studies. PMID:26624015

  16. CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases.

    PubMed

    V, Alexandar; Nayar, Pradeep G; Murugesan, R; Mary, Beaulah; P, Darshana; Ahmed, Shiek S S J

    2015-01-01

    Cardiovascular diseases (CVDs) account for high morbidity and mortality worldwide. Both, genetic and epigenetic factors are involved in the enumeration of various cardiovascular diseases. In recent years, a vast amount of multi-omics data are accumulated in the field of cardiovascular research, yet the understanding of key mechanistic aspects of CVDs remain uncovered. Hence, a comprehensive online resource tool is required to comprehend previous research findings and to draw novel methodology for understanding disease pathophysiology. Here, we have developed a literature-based database, CardioGenBase, collecting gene-disease association from Pubmed and MEDLINE. The database covers major cardiovascular diseases such as cerebrovascular disease, coronary artery disease (CAD), hypertensive heart disease, inflammatory heart disease, ischemic heart disease and rheumatic heart disease. It contains ~1,500 cardiovascular disease genes from ~2,4000 research articles. For each gene, literature evidence, ontology, pathways, single nucleotide polymorphism, protein-protein interaction network, normal gene expression, protein expressions in various body fluids and tissues are provided. In addition, tools like gene-disease association finder and gene expression finder are made available for the users with figures, tables, maps and venn diagram to fit their needs. To our knowledge, CardioGenBase is the only database to provide gene-disease association for above mentioned major cardiovascular diseases in a single portal. CardioGenBase is a vital online resource to support genome-wide analysis, genetic, epigenetic and pharmacological studies. PMID:26624015

  17. PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

    PubMed

    Paul, Sandip; Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V; Chattopadhyay, Sujay

    2015-12-01

    A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. PMID:26456591

  18. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    DOE PAGESBeta

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; USA, Richland Washington; Bonneville, Alain; USA, Richland Washington; Sullivan, E. Charlotte; USA, Richland Washington; Johnson, Tim C.; USA, Richland Washington; et al

    2014-12-31

    A comprehensive monitoring program will be needed in order to assess the effectiveness of carbon sequestration at the FutureGen 2.0 carbon capture and storage (CCS) field-site. Geophysical monitoring methods are sensitive to subsurface changes that result from injection of CO2 and will be used for: (1) tracking the spatial extent of the free phase CO2 plume, (2) monitoring advancement of the pressure front, (3) identifying or mapping areas where induced seismicity occurs, and (4) identifying and mapping regions of increased risk for brine or CO2 leakage from the reservoir. Site-specific suitability and cost effectiveness were evaluated for a number ofmore » geophysical monitoring methods including: passive seismic monitoring, reflection seismic imaging, integrated surface deformation, time-lapse gravity, pulsed neutron capture logging, cross-borehole seismic, electrical resistivity tomography, magnetotellurics and controlled source electromagnetics. The results of this evaluation indicate that CO2 injection monitoring using reflection seismic methods would likely be difficult at the FutureGen 2.0 site. Electrical methods also exhibited low sensitivity to the expected CO2 saturation changes and would be affected by metallic infrastructure at the field site. Passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture monitoring were selected for implementation as part of the FutureGen 2.0 storage site monitoring program.« less

  19. Geophysical Monitoring Methods Evaluation for the FutureGen 2.0 Project

    SciTech Connect

    Strickland, Chris E.; USA, Richland Washington; Vermeul, Vince R.; USA, Richland Washington; Bonneville, Alain; USA, Richland Washington; Sullivan, E. Charlotte; USA, Richland Washington; Johnson, Tim C.; USA, Richland Washington; Spane, Frank A.; USA, Richland Washington; Gilmore, Tyler J.; USA, Richland Washington

    2014-12-31

    A comprehensive monitoring program will be needed in order to assess the effectiveness of carbon sequestration at the FutureGen 2.0 carbon capture and storage (CCS) field-site. Geophysical monitoring methods are sensitive to subsurface changes that result from injection of CO2 and will be used for: (1) tracking the spatial extent of the free phase CO2 plume, (2) monitoring advancement of the pressure front, (3) identifying or mapping areas where induced seismicity occurs, and (4) identifying and mapping regions of increased risk for brine or CO2 leakage from the reservoir. Site-specific suitability and cost effectiveness were evaluated for a number of geophysical monitoring methods including: passive seismic monitoring, reflection seismic imaging, integrated surface deformation, time-lapse gravity, pulsed neutron capture logging, cross-borehole seismic, electrical resistivity tomography, magnetotellurics and controlled source electromagnetics. The results of this evaluation indicate that CO2 injection monitoring using reflection seismic methods would likely be difficult at the FutureGen 2.0 site. Electrical methods also exhibited low sensitivity to the expected CO2 saturation changes and would be affected by metallic infrastructure at the field site. Passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture monitoring were selected for implementation as part of the FutureGen 2.0 storage site monitoring program.

  20. Enhanced and synthetic vision for terminal maneuvering area NextGen operations

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Norman, R. Michael; Williams, Steven P.; Arthur, Jarvis J., III; Shelton, Kevin J.; Prinzel, Lawrence J., III

    2011-06-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility ground (taxi) operations and approach/landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for EFVS for operations in visibility as low as 1000 ft runway visibility range (RVR) and SVS to enable lower decision heights (DH) than can currently be flown today. Expanding the EFVS visual segment from DH to the runway in visibilities as low as 1000 RVR appears to be viable as touchdown performance was excellent without any workload penalties noted for the EFVS concept tested. A lower DH to 150 ft and/or possibly reduced visibility minima by virtue of SVS equipage appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  1. Leptojacobus dorci n. gen., n. sp. (Nematoda: Diplogastridae), an Associate of Dorcus Stag Beetles (Coleoptera: Lucanidae)

    PubMed Central

    Kanzaki, Natsumi; Ragsdale, Erik J.; Susoy, Vladislav; Sommer, Ralf J.

    2014-01-01

    A new species of diplogastrid nematode, Leptojacobus dorci n. gen., n. sp., was isolated from adults of the stag beetle Dorcus ritsemae (Coleoptera: Lucanidae) that were purchased from a pet shop in Japan. Leptojacobus n. gen. is circumscribed by a very thin, delicate body and by a small stoma with minute armature. A combination of other stomatal characters, namely the division of the cheilostom into adradial plates, the symmetry of the subventral stegostomatal sectors, and the presence of a thin, conical dorsal tooth, further distinguishes Leptojacobus n. gen. from other genera of Diplogastridae. Phylogenetic analysis of nearly full-length SSU rRNA sequences support the new species, together with an isolate identified previously as Koerneria luziae, to be excluded from a clade including all other molecularly characterized diplogastrids with teeth and stomatal dimorphism. Therefore, the new species will be of importance for reconstruction of ancestral character histories in Diplogastridae, a family circumscribed by a suite of feeding-related novelties. PMID:24644371

  2. FutureGen: Stepping-Stone to Sustainable Fossil-Fuel Power Generation

    SciTech Connect

    Zitney, S.E.

    2006-11-01

    This presentation will highlight the U.S. Department of Energy's FutureGen Initiative. The nearly $1 billion government-industry project is a stepping-stone toward future coal-fired power plants that will produce hydrogen and electricity with zero-emissions, including carbon dioxide. The 275-megawatt FutureGen plant will initiate operations around 2012 and employ advanced coal gasification technology integrated with combined cycle electricity generation, hydrogen production, and carbon capture and sequestration. The initiative is a response to a presidential directive to develop a hydrogen economy by drawing upon the best scientific research to address the issue of global climate change. The FutureGen plant will be based on cutting-edge power generation technology as well as advanced carbon capture and sequestration systems. The centerpiece of the project will be coal gasification technology that can eliminate common air pollutants such as sulfur dioxide and nitrogen oxides and convert them to useable by-products. Gasification will convert coal into a highly enriched hydrogen gas, which can be burned much more cleanly than directly burning the coal itself. Alternatively, the hydrogen can be used in a fuel cell to produce ultra-clean electricity, or fed to a refinery to help upgrade petroleum products. Carbon sequestration will also be a key feature that will set the Futuregen plant apart from other electric power plant projects. The initial goal will be to capture 90 percent of the plant's carbon dioxide, but capture of nearly 100 percent may be possible with advanced technologies. Once captured, the carbon dioxide will be injected as a compressed fluid deep underground, perhaps into saline reservoirs. It could even be injected into oil or gas reservoirs, or into unmineable coal seams, to enhance petroleum or coalbed methane recovery. The ultimate goal for the FutureGen plant is to show how new technology can eliminate environmental concerns over the future use of coal--the most abundant fossil fuel in the United States with supplies projected to last 250 years. FutureGen's co-production of power and hydrogen will also serve as a stepping-stone to an environmentally sustainable energy future.

  3. Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup.

    PubMed

    Overby, C L; Heale, B; Aronson, S; Cherry, J M; Dwight, S; Milosavljevic, A; Nelson, T; Niehaus, A; Weaver, M A; Ramos, E M; Williams, M S

    2016-02-01

    The Clinical Genome Resource (ClinGen) is a National Institutes of Health (NIH)-funded collaborative program that brings together a variety of projects designed to provide high-quality, curated information on clinically relevant genes and variants. ClinGen's EHR (Electronic Health Record) Workgroup aims to ensure that ClinGen is accessible to providers and patients through EHR and related systems. This article describes the current scope of these efforts and progress to date. The ClinGen public portal can be accessed at www.clinicalgenome.org. PMID:26418054

  4. Data-link and surface map traffic intent displays for NextGen 4DT and equivalent visual surface operations

    NASA Astrophysics Data System (ADS)

    Shelton, Kevin J.; Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J., III; Jones, Denise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-05-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a consortium of industry, academia and government agencies have proposed a revolutionary new concept for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the concept of "net-centric" operations whereby each aircraft and air services provider shares information to allow real-time adaptability to ever-changing factors such as weather, traffic, flight trajectories, and security. Data-link is likely to be the primary source of communication in NextGen. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen.

  5. Roles of SLX1-SLX4, MUS81-EME1, and GEN1 in avoiding genome instability and mitotic catastrophe.

    PubMed

    Sarbajna, Shriparna; Davies, Derek; West, Stephen C

    2014-05-15

    The resolution of recombination intermediates containing Holliday junctions (HJs) is critical for genome maintenance and proper chromosome segregation. Three pathways for HJ processing exist in human cells and involve the following enzymes/complexes: BLM-TopoIII?-RMI1-RMI2 (BTR complex), SLX1-SLX4-MUS81-EME1 (SLX-MUS complex), and GEN1. Cycling cells preferentially use the BTR complex for the removal of double HJs in S phase, with SLX-MUS and GEN1 acting at temporally distinct phases of the cell cycle. Cells lacking SLX-MUS and GEN1 exhibit chromosome missegregation, micronucleus formation, and elevated levels of 53BP1-positive G1 nuclear bodies, suggesting that defects in chromosome segregation lead to the transmission of extensive DNA damage to daughter cells. In addition, however, we found that the effects of SLX4, MUS81, and GEN1 depletion extend beyond mitosis, since genome instability is observed throughout all phases of the cell cycle. This is exemplified in the form of impaired replication fork movement and S-phase progression, endogenous checkpoint activation, chromosome segmentation, and multinucleation. In contrast to SLX4, SLX1, the nuclease subunit of the SLX1-SLX4 structure-selective nuclease, plays no role in the replication-related phenotypes associated with SLX4/MUS81 and GEN1 depletion. These observations demonstrate that the SLX1-SLX4 nuclease and the SLX4 scaffold play divergent roles in the maintenance of genome integrity in human cells. PMID:24831703

  6. Data-Link and Surface Map Traffic Intent Displays for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Prinzel, Lawrence J., III; Arthur, Jarvis J., III; Jones, Deise R.; Allamandola, Angela S.; Bailey, Randall E.

    2009-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a consortium of industry, academia and government agencies have proposed a revolutionary new concept for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the concept of "net-centric" operations whereby each aircraft and air services provider shares information to allow real-time adaptability to ever-changing factors such as weather, traffic, flight trajectories, and security. Data-link is likely to be the primary source of communication in NextGen. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen.

  7. GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes.

    PubMed

    Freeman, Alasdair D J; Liu, Yijin; Déclais, Anne-Cécile; Gartner, Anton; Lilley, David M J

    2014-12-12

    Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1nt 3' to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1. PMID:25315822

  8. GEN1 from a Thermophilic Fungus Is Functionally Closely Similar to Non-Eukaryotic Junction-Resolving Enzymes

    PubMed Central

    Freeman, Alasdair D.J.; Liu, Yijin; Dclais, Anne-Ccile; Gartner, Anton; Lilley, David M.J.

    2014-01-01

    Processing of Holliday junctions is essential in recombination. We have identified the gene for the junction-resolving enzyme GEN1 from the thermophilic fungus Chaetomium thermophilum and expressed the N-terminal 487-amino-acid section. The protein is a nuclease that is highly selective for four-way DNA junctions, cleaving 1nt 3? to the point of strand exchange on two strands symmetrically disposed about a diagonal axis. CtGEN1 binds to DNA junctions as a discrete homodimer with nanomolar affinity. Analysis of the kinetics of cruciform cleavage shows that cleavage of the second strand occurs an order of magnitude faster than the first cleavage so as to generate a productive resolution event. All these properties are closely similar to those described for bacterial, phage and mitochondrial junction-resolving enzymes. CtGEN1 is also similar in properties to the human enzyme but lacks the problems with aggregation that currently prevent detailed analysis of the latter protein. CtGEN1 is thus an excellent enzyme with which to engage in biophysical and structural analysis of eukaryotic GEN1. PMID:25315822

  9. Next Gen NEAR: Near Earth Asteroid Human Robotic Precursor Mission Concept

    NASA Technical Reports Server (NTRS)

    Rivkin, Andrew S.; Kirby, Karen; Cheng, Andrew F.; Gold, Robert; Kelly, Daniel; Reed, Cheryl; Abell, Paul; Garvin, James; Landis, Rob

    2012-01-01

    Asteroids have long held the attention of the planetary science community. In particular, asteroids that evolve into orbits near that of Earth, called near-Earth objects (NEO), are of high interest as potential targets for exploration due to the relative ease (in terms of delta V) to reach them. NASA's Flexible Path calls for missions and experiments to be conducted as intermediate steps towards the eventual goal of human exploration of Mars; piloted missions to NEOs are such example. A human NEO mission is a valuable exploratory step beyond the Earth-Moon system enhancing capabilities that surpass our current experience, while also developing infrastructure for future mars exploration capabilities. To prepare for a human rendezvous with an NEO, NASA is interested in pursuing a responsible program of robotic NEO precursor missions. Next Gen NEAR is such a mission, building on the NEAR Shoemaker mission experience at the JHU/APL Space Department, to provide an affordable, low risk solution with quick data return. Next Gen NEAR proposes to make measurements needed for human exploration to asteroids: to demonstrate proximity operations, to quantify hazards for human exploration and to characterize an environment at a near-Earth asteroid representative of those that may be future human destinations. The Johns Hopkins University Applied Physics Laboratory has demonstrated exploration-driven mission feasibility by developing a versatile spacecraft design concept using conventional technologies that satisfies a set of science, exploration and mission objectives defined by a concept development team in the summer of 2010. We will describe the mission concept and spacecraft architecture in detail. Configuration options were compared with the mission goals and objectives in order to select the spacecraft design concept that provides the lowest cost, lowest implementation risk, simplest operation and the most benefit for the mission implementation. The Next Gen NEAR spacecraft was designed to support rendezvous with a range of candidate asteroid targets and could easily be launched with one of several NASA launch vehicles. The Falcon 9 launch vehicle supports a Next Gen NEAR launch to target many near-Earth asteroids under consideration that could be reached with a C3 of 18 km2/sec2 or less, and the Atlas V-401 provides added capability supporting launch to NEAs that require more lift capacity while at the same time providing such excess lift capability that another payload of opportunity could be launch in conjunction with Next Gen NEAR. Next Gen NEAR will measure and interact with the target surface in ways never undertaken at an asteroid, and will prepare for first human precursor mission by demonstrating exploration science operations at an accessible NEO. This flexible mission and spacecraft design concept supports target selection based on upcoming Earth-based observations and also provides opportunities for co-manifest & international partnerships. JHU/APL has demonstrated low cost, low risk, high impact missions and this mission will help to prepare NASA for human NEO exploration by combining the best of NASA s human and robotic exploration capabilities.

  10. Enhanced Flight Vision Systems and Synthetic Vision Systems for NextGen Approach and Landing Operations

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Bailey, Randall E.; Ellis, Kyle K. E.; Williams, Steven P.; Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Shelton, Kevin J.

    2013-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment with equivalent efficiency as visual operations. To meet this potential, research is needed for effective technology development and implementation of regulatory standards and design guidance to support introduction and use of SVS/EFVS advanced cockpit vision technologies in Next Generation Air Transportation System (NextGen) operations. A fixed-base pilot-in-the-loop simulation test was conducted at NASA Langley Research Center that evaluated the use of SVS/EFVS in NextGen low visibility approach and landing operations. Twelve crews flew approach and landing operations in a simulated NextGen Chicago O'Hare environment. Various scenarios tested the potential for using EFVS to conduct approach, landing, and roll-out operations in visibility as low as 1000 feet runway visual range (RVR). Also, SVS was tested to evaluate the potential for lowering decision heights (DH) on certain instrument approach procedures below what can be flown today. Expanding the portion of the visual segment in which EFVS can be used in lieu of natural vision from 100 feet above the touchdown zone elevation to touchdown and rollout in visibilities as low as 1000 feet RVR appears to be viable as touchdown performance was acceptable without any apparent workload penalties. A lower DH of 150 feet and/or possibly reduced visibility minima using SVS appears to be viable when implemented on a Head-Up Display, but the landing data suggests further study for head-down implementations.

  11. Gen IV Materials Handbook Functionalities and Operation (4A) Handbook Version 4.0

    SciTech Connect

    Ren, Weiju

    2013-09-01

    This document is prepared for navigation and operation of the Gen IV Materials Handbook, with architecture description and new user access initiation instructions. Development rationale and history of the Handbook is summarized. The major development aspects, architecture, and design principles of the Handbook are briefly introduced to provide an overview of its past evolution and future prospects. Detailed instructions are given with examples for navigating the constructed Handbook components and using the main functionalities. Procedures are provided in a step-by-step fashion for Data Upload Managers to upload reports and data files, as well as for new users to initiate Handbook access.

  12. Modeling Off-Nominal Recovery in NextGen Terminal-Area Operations

    NASA Technical Reports Server (NTRS)

    Callantine, Todd J.

    2011-01-01

    Robust schedule-based arrival management requires efficient recovery from off-nominal situations. This paper presents research on modeling off-nominal situations and plans for recovering from them using TRAC, a route/airspace design, fast-time simulation, and analysis tool for studying NextGen trajectory-based operations. The paper provides an overview of a schedule-based arrival-management concept and supporting controller tools, then describes TRAC implementations of methods for constructing off-nominal scenarios, generating trajectory options to meet scheduling constraints, and automatically producing recovery plans.

  13. Irradiation effects in oxide dispersion strengthened (ODS) Ni-base alloys for Gen. IV nuclear reactors

    NASA Astrophysics Data System (ADS)

    Oono, Naoko; Ukai, Shigeharu; Kondo, Sosuke; Hashitomi, Okinobu; Kimura, Akihiko

    2015-10-01

    Oxide particle dispersion strengthened (ODS) Ni-base alloys are irradiated by using simulation technique (Fe/He dual-ion irradiation) to investigate the reliability to Gen. IV high-temperature reactors. The fine oxide particles with less than 10nm in average size and approximately 8.0נ1022m-3 in number density remained after 101dpa irradiation. The tiny helium bubbles were inside grains, not at grain-boundaries; it is advantageous effect of oxide particles which trap the helium atoms at the particle-matrix interface. Ni-base ODS alloys demonstrated their great ability to overcome He embrittlement.

  14. Evaluation of Gen-Probe's Histoplasma capsulatum and Cryptococcus neoformans AccuProbes.

    PubMed Central

    Huffnagle, K E; Gander, R M

    1993-01-01

    Gen-Probe's DNA probes were evaluated for use in the identification of clinical isolates of Histoplasma capsulatum var. capsulatum and Cryptococcus neoformans. Ninety-five mould-phase fungi were probed, including 41 isolates of H. capsulatum var. capsulatum. Similarly, 98 yeasts, including 42 C. neoformans isolates, were examined by using the C. neoformans DNA probe. In the study, both probes demonstrated 100% specificity and 100% sensitivity. Their use in the clinical laboratory may significantly reduce the time required for definitive identification of fungi. PMID:8432829

  15. Bias explorer: measurements of compositional bias in EMBL and GenBank sequence files.

    PubMed

    Fuglsang, Anders

    2004-11-01

    A Windows application for compositional analysis of sequenced genomes (EMBL or GenBank flat files) is available as freeware. The application allows the user to quantify word bias using Markov chain analysis and it allows the user to generate sliding window data for GC-skew, AT-skew, purine excess, keto excess and discrete word counts. The mathematical routines reside in a dynamic link library (DLL), which can be used independently by other applications. The software is available for download at http://www.dfuni.dk/~anfu/Bioinformatics/Main.htm. PMID:15702383

  16. Considerations of Alloy 617 Application in the Gen IV Nuclear Reactor Systems - Part I: Mechanical Property Challenges

    SciTech Connect

    Ren, Weiju

    2010-01-01

    Alloy 617 is currently considered as a leading candidate material for high temperature components in the Gen IV Nuclear Reactor Systems. Because of the unprecedented severe working conditions beyond its commercial service experience required by the Gen IV systems, the alloy faces various challenges in both mechanical and metallurgical properties. This paper, as Part I of the discussion, is focused on the challenges and issues in the mechanical properties of Alloy 617 for the intended nuclear application. Considerations are given in details in its mechanical property data scatter, low creep strength in the desired high temperature range, lack of longterm creep curves, high loading rate dependency, and preponderant tertiary creep. Some research and development activities are suggested with discussions on their viability to satisfy the Gen IV Nuclear Reactor System needs in near future and in the long run.

  17. Considerations of Alloy 617 Application in the Gen IV Nuclear Reactor Systems - Part II: Metallurgical Property Challenges

    SciTech Connect

    Ren, Weiju

    2010-01-01

    Alloy 617 is currently considered as a leading candidate material for high temperature components in the Gen IV Nuclear Reactor Systems. Because of the unprecedented severe working conditions beyond its commercial service experience required by the Gen IV systems, the alloy faces various challenges in both mechanical and metallurgical properties. Following a previous paper discussing the mechanical property challenges, this paper is focused on the challenges and issues in metallurgical properties of the alloy for the intended nuclear application. Considerations are given in details about its metallurgical stability and aging evolution, aging effects on mechanical properties, potential Co hazard, and internal oxidation. Some research and development activities are suggested with discussions on viability to satisfy the Gen IV Nuclear Reactor System needs.

  18. LungGENS: a web-based tool for mapping single-cell gene expression in the developing lung

    PubMed Central

    Du, Yina; Guo, Minzhe; Whitsett, Jeffrey A; Xu, Yan

    2015-01-01

    We developed LungGENS (Lung Gene Expression iN Single-cell), a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables. LungGENS will be broadly applicable in respiratory research, providing a cell-specific RNA expression resource at single-cell resolution. LungGENS is freely available for non-commercial use at https://research.cchmc.org/pbge/lunggens/default.html. PMID:26130332

  19. 'LungGENS': a web-based tool for mapping single-cell gene expression in the developing lung.

    PubMed

    Du, Yina; Guo, Minzhe; Whitsett, Jeffrey A; Xu, Yan

    2015-11-01

    We developed LungGENS (Lung Gene Expression iN Single-cell), a web-based bioinformatics resource for querying single-cell gene expression databases by entering a gene symbol or a list of genes or selecting a cell type of their interest. Gene query provides quantitative RNA expression of the gene of interest in each lung cell type. Cell type query returns associated selective gene signatures and genes encoding cell surface markers and transcription factors in interactive heatmap and tables. LungGENS will be broadly applicable in respiratory research, providing a cell-specific RNA expression resource at single-cell resolution. LungGENS is freely available for non-commercial use at https://research.cchmc.org/pbge/lunggens/default.html. PMID:26130332

  20. Application of part-whole training methods to evaluate when to introduce NextGen air traffic management tools to students.

    PubMed

    Vu, Kim-Phuong L; Kiken, Ariana; Chiappe, Dan; Strybel, Thomas Z; Battiste, Vernol

    2013-01-01

    The Next Generation Air Transportation System (NextGen) will use advanced technologies and new concepts of operation to accommodate projected increases in air travel over the next few decades. Use of NextGen tools requires air traffic controllers (ATCos) to use different procedures than those required to manage NextGen-unequipped aircraft, and ATCos will need to integrate the 2 skill sets when managing a sector consisting of NextGen-equipped and unequipped aircraft. The goal of the present study was to determine the effectiveness of 2 procedures in the training of student controllers to manage both equipage types. We applied a variant of the part-whole training paradigm in the present study. Using a quasi-experimental design, we trained students from 2 different labs of an internship course to manage air traffic with potential NextGen tools concurrent with their traditional training (whole-task group) or after they had time to learn traditional air traffic management skills (part-whole group). Participants were then tested in their ability to manage a simulated sector consisting of different percentages of NextGen-equipped and unequipped aircraft at the mid-term and after the final week of their internship. Results showed that it is better to train students in manual ATCo skills before introducing NextGen tools, unless the students are of higher aptitude. For more skilled students, simultaneously introducing NextGen and manual tools into their curriculum had little negative impact. PMID:24455810

  1. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

    PubMed Central

    Doniger, Scott W; Salomonis, Nathan; Dahlquist, Kam D; Vranizan, Karen; Lawlor, Steven C; Conklin, Bruce R

    2003-01-01

    MAPPFinder is a tool that creates a global gene-expression profile across all areas of biology by integrating the annotations of the Gene Ontology (GO) Project with the free software package GenMAPP . The results are displayed in a searchable browser, allowing the user to rapidly identify GO terms with over-represented numbers of gene-expression changes. Clicking on GO terms generates GenMAPP graphical files where gene relationships can be explored, annotated, and files can be freely exchanged. PMID:12540299

  2. A REVIEW ON CURRENT STATUS OF ALLOYS 617 AND 230 FOR GEN IV NUCLEAR REACTOR INTERNALS AND HEAT EXCHANGERS

    SciTech Connect

    Ren, Weiju; Swindeman, Robert W

    2009-01-01

    Alloys 617 and 230 are currently identified as two leading candidate metallic materials in the down selection for applications at temperatures above 760 C in the Gen IV Nuclear Reactor Systems. Qualifying the materials requires significant information related to Codification, mechanical behavior modeling, metallurgical stability, environmental resistance, and many other aspects. In the present paper, material requirements for the Gen IV Nuclear Reactor Systems are discussed; certain available information regarding the two alloys under consideration for the intended applications are reviewed and analyzed. Suggestions are presented for further R&D activities for the materials selection.

  3. Brockphasma spinifemoralis gen. et spec. nov.: a new phasmid genus and new species of Neohiraseini (Phasmida: Necrosciinae) from Vietnam.

    PubMed

    Ho, George Wai-Chun; Liu, Xing-Yue; Bresseel, Joachim; Constant, Jerome

    2014-01-01

    A new genus of stick insects, Brockphasma Ho gen. nov., with the type-species, Brockphasma spinifemoralis Ho, Liu, Bresseel & Constant spec. nov., is described and illustrated from Vietnam. Both sexes, the egg and the first instar nymph are described and figured. Data on the habitat and natural foodplants are provided. Brockphasma Ho gen. nov. is differentiated from other genera in Neohiraseini by spinose occiput, anterior region of mesonotum with a spinose hump and spinose anterodorsal and posterodorsal carinae of femora. A key to the genera of Neohiraseini from Vietnam is given. PMID:24990046

  4. Structures and stability of metal-doped GenM (n = 9, 10) clusters

    DOE PAGESBeta

    Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

    2015-06-26

    The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Suchmore » cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

  5. The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

    PubMed

    Sundell, David; Mannapperuma, Chanaka; Netotea, Sergiu; Delhomme, Nicolas; Lin, Yao-Cheng; Sjödin, Andreas; Van de Peer, Yves; Jansson, Stefan; Hvidsten, Torgeir R; Street, Nathaniel R

    2015-12-01

    Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight. PMID:26192091

  6. Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 Performance Evaluation Final Report

    SciTech Connect

    Jon P. Christophersen; Ira Bloom; Edward V. Thomas; Kevin L. Gering; Gary L. Henriksen; Vincent S. Battaglia; David Howell

    2006-07-01

    The Advanced Technology Development Program has completed performance testing of the second generation of lithium-ion cells (i.e., Gen 2 cells). The 18650-size Gen 2 cells, with a baseline and variant chemistry, were distributed over a matrix consisting of three states-of-charge (SOCs) (60, 80, and 100% SOC), four temperatures (25, 35, 45, and 55C), and three life tests (calendar-, cycle-, and accelerated-life). The calendar- and accelerated-life cells were clamped at an open-circuit voltage corresponding to the designated SOC and were subjected to a once-per-day pulse profile. The cycle-life cells were continuously pulsed using a profile that was centered around 60% SOC. Life testing was interrupted every four weeks for reference performance tests (RPTs), which were used to quantify changes in cell degradation as a function of aging. The RPTs generally consisted of C1/1 and C1/25 static capacity tests, a low-current hybrid pulse power characterization test, and electrochemical impedance spectroscopy. The rate of cell degradation generally increased with increasing test temperature, and SOC. It was also usually slowest for the calendar-life cells and fastest for the accelerated-life cells. Detailed capacity-, power-, and impedance-based performance results are reported.

  7. Advanced Technology Development Program for Lithium-Ion Batteries: Gen 2 GDR Performance Evaluation Report

    SciTech Connect

    Jon P. Christophersen; Chinh D. Ho; Gary L. Henriksen; David Howell

    2006-07-01

    The Advanced Technology Development Program has completed the performance evaluation of the second generation of lithium-ion cells (i.e., Gen 2 cells). This report documents the testing and analysis of the Gen 2 GDR cells, which were used to learn and debug the newly developed Technology Life Verification Test Manual. The purpose of the manual is to project a 15-year, 150,000 mile battery life capability with a 90% confidence interval using predictive models and short-term testing. The GDR cells were divided into two different matrices. The core-life test matrix consisted of calendar- and cycle-life cells with various changes to the four major acceleration factors (temperature, state-of-charge, throughput, and power rating). The supplemental-life test matrix consisted of cells subjected either to a path dependence study, or a comparison between the standard hybrid pulse power characterization test and the newly-developed minimum pulse power characterization test. Resistance and capacity results are reported.

  8. Structural materials for Gen-IV nuclear reactors: Challenges and opportunities

    NASA Astrophysics Data System (ADS)

    Murty, K. L.; Charit, I.

    2008-12-01

    Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses and extremely corrosive environment, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This paper presents a summary of various Gen-IV reactor concepts, with emphasis on the structural materials issues depending on the specific application areas. This paper also discusses the challenges involved in using the existing materials under both service and off-normal conditions. Tasks become increasingly complex due to the operation of various fundamental phenomena like radiation-induced segregation, radiation-enhanced diffusion, precipitation, interactions between impurity elements and radiation-produced defects, swelling, helium generation and so forth. Further, high temperature capability (e.g. creep properties) of these materials is a critical, performance-limiting factor. It is demonstrated that novel alloy and microstructural design approaches coupled with new materials processing and fabrication techniques may mitigate the challenges, and the optimum system performance may be achieved under much demanding conditions.

  9. Paragnomoxyala gen. nov. (Xyalidae, Monhysterida, Nematoda) from the East China Sea.

    PubMed

    Jiang, Weijun; Huang, Yong

    2015-01-01

    A new genus, Paragnomoxyala gen. nov., and a new species, Paragnomoxyala breviseta sp. nov. are described from the East China Sea. Paragnomoxyala gen. nov. is characterized by having large funnel-shaped buccal cavity with cuticularized walls and extended anteriorly; lips very high; striated cuticle; four cephalic setae, absence of outer labial setae; circular amphidial fovea; straight spicules and absence of gubernaculum; tail conico-cylindrical with three terminal setae; female monodelphic with an anterior outstretched ovary. It differs from similar genera by having a large buccal cavity unique in Xyalidae, straight spicules, lacking gubernaculum, and conico-cylindrical tail with terminal setae. Paragnomoxyala breviseta sp. nov. is characterized by having a large funnel-shaped buccal cavity, with cuticularized walls and extended anteriorly, 1.6-1.8 hd long and 63-79% cbd wide; four cephalic setae 3-4 m long; circular amphids 6-9 m in diameter; spicules straight but slightly bent at both ends; absence of gubernaculum and precloacal supplement. PMID:26624631

  10. Flight Deck Technologies to Enable NextGen Low Visibility Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence (Lance) J., III; Arthur, Jarvis (Trey) J.; Kramer, Lynda J.; Norman, Robert M.; Bailey, Randall E.; Jones, Denise R.; Karwac, Jerry R., Jr.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2013-01-01

    Many key capabilities are being identified to enable Next Generation Air Transportation System (NextGen), including the concept of Equivalent Visual Operations (EVO) . replicating the capacity and safety of today.s visual flight rules (VFR) in all-weather conditions. NASA is striving to develop the technologies and knowledge to enable EVO and to extend EVO towards a Better-Than-Visual operational concept. This operational concept envisions an .equivalent visual. paradigm where an electronic means provides sufficient visual references of the external world and other required flight references on flight deck displays that enable Visual Flight Rules (VFR)-like operational tempos while maintaining and improving safety of VFR while using VFR-like procedures in all-weather conditions. The Langley Research Center (LaRC) has recently completed preliminary research on flight deck technologies for low visibility surface operations. The work assessed the potential of enhanced vision and airport moving map displays to achieve equivalent levels of safety and performance to existing low visibility operational requirements. The work has the potential to better enable NextGen by perhaps providing an operational credit for conducting safe low visibility surface operations by use of the flight deck technologies.

  11. 76 FR 28973 - Terra-Gen Dixie Valley, LLC; Order on Rehearing and Accepting Tariff Filing, Subject to...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-19

    ... Federal Register, 76 FR 16,621 (2011), with interventions and protests due on or before April 6, 2011. On... Public Utilities and Transmitting Utilities, Order No. 888, 61 FR 21,540 (May 10, 1996), FERC Stats... consistent with or superior to the pro forma OATT. The Commission directed Terra Gen to resubmit an OATT...

  12. Gen Green: Changes in Australian Apprentices' and Trainees' Experience of Skills and Sustainability from 2008 to 2011

    ERIC Educational Resources Information Center

    Sack, Fabian

    2012-01-01

    The Gen Green research in 2008 and 2011 indicates that skills for sustainability public policy and business initiatives are having an impact, but that young skilled Australians' high level of interest in sustainability skills is confounded by a lack of guidance and incentives from employers, the market and educators. The research indicates that,

  13. A review of Chinese tribe Achilini (Hemiptera: Fulgoromorpha: Achilidae),
    with descriptions of Paracatonidia webbeda gen. & sp. nov.

    PubMed

    Long, Jian-Kun; Yang, Lin; Chen, Xiang-Sheng

    2015-01-01

    Planthoppers of the tribe Achilini (Hemiptera: Fulgoromorpha: Achilidae) from China, are reviewed. A key to the three genera of Chinese Achilini is given. A new genus and species of the tribe from southwestern China: Paracatonidia webbeda gen. & sp. nov., is described. A new genus and species record for China, Cixidia kasparyani Anufriev, is also given. PMID:26701421

  14. OmniGen-AF supplementation modulated the physiological and acute phase responses of Brahman heifers to an endotoxin challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the physiological and acute phase responses (APR) of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 183±5 kilograms) from the Texas AgriLife Research Center in Overton...

  15. Enhancement of the acute phase response to lipopolysaccharide in feedlot steers supplemented with OmniGen-AF

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study was designed to determine the effect of supplementing feedlot steers with OmniGen-AF on the acute phase response to a lipopolysaccharide (LPS) challenge. Steers (n = 18; 270 ± 5 kilograms body weight) were separated into two treatment groups (n=9/treatment): one group was fed a standard ...

  16. YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps.

    PubMed

    Batesole, Keith; Wimalanathan, Kokulapalan; Liu, Lin; Zhang, Fan; Echt, Craig S; Liang, Chun

    2014-01-01

    Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are uploaded, either publically or privately, as long as they follow our template which is available in several standard file formats. Data is parsed and loaded into MySQL relational database to be displayed and compared against users' genetic maps or other public data available on YouGenMap. With the highly interactive GUIs, all public data on YouGenMap are maps available for visualization, comparison, search, filtration and download. YouGenMap web tool is available on the website (http://conifergdb.miamioh.edu/yougenmap) with the source-code repository at (http://sourceforge.net/projects/yougenmap/?source=directory). PMID:25009553

  17. Modulation of the metabolic response to an endotoxin challenge in Brahman heifers through OmniGen-AF supplementation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study examined the effect of feeding OmniGen-AF (OG; Prince Agri Products) on the metabolic response of newly-weaned heifers to an endotoxin (lipopolysaccharide; LPS) challenge. Brahman heifers (n=24; 1835 kilograms) from the Texas AgriLife Research Center in Overton, TX, were separated into 2...

  18. An update on VitisGen: recent advances in using DNA marker technologies in U.S. grape breeding programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA-NIFA VitisGen project involves a multidisciplinary team of 25 co-PIs at 11 institutions aiming to optimize grape cultivar improvement. To this end, an impressive collection of phenotypic data and high-resolution genetic maps has been developed for seventeen F1 families. Here, we will prese...

  19. 75 FR 1052 - Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New York Canyon, LLC; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-08

    ... intervention to the Federal Energy Regulatory Commission, 888 First Street, NE., Washington, DC 20426. This... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Terra-Gen Dixie Valley, LLC; TGP Dixie Development Company, LLC; New...

  20. A Phocus on Phenotyping: opportunities and challenges in local and centralized trait evaluation from the VitisGen experience

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The integration of relevant genetic resources, robust phenotypes, and cutting-edge genotypic data is a challenge that individual scientists rarely overcome successfully. In the USDA-NIFA VitisGen project ( www.vitisgen.org ) for grapevine cultivar improvement, our research team has pursued a shared ...

  1. Pulicitrogus compressus gen. nov., sp. nov. (Copepoda, Siphonostomatoida, Artotrogidae) associated with an ascidian in the Sea of Japan

    NASA Astrophysics Data System (ADS)

    Kim, Il-Hoi

    1998-06-01

    Pulicitrogus compressus gen. nov., sp. nov., an ecto-associate of the ascidian Halocynthia hilgendorfi igaboja (Oka), is described on the basis of female and male specimens from the Korean coast of the Sea of Japan. This copepod is unique in having a laterally compressed body, with a reduced armature on the legs.

  2. 75 FR 5780 - Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-04

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Green Borders Geothermal, LLC, Complainant, v. Terra-Gen Dixie Valley, LLC, Respondent; Notice of Complaint January 28, 2010. Take notice that on January 25, 2010, Green Borders Geothermal, LLC (Green Borders) filed...

  3. Rationale and Design of the National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) Registry

    PubMed Central

    2010-01-01

    Background Although the management of thoracic aortic aneurysms (TAAs) has improved significantly, patients presenting with aortic dissections, rupture or other acute complications of TAAs continue to suffer high rates of morbidity and mortality. Accumulating data have indicated that many TAAs are due to underlying gene mutations. A comprehensive approach to the study of TAAs resulting from genetic mutations is needed to translate this information into advances in treatment. Objective The National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) was established to provide a biospecimen inventory and bioinformatics infrastructure to enable research to advance the clinical management of genetically-triggered TAAs and related complications. Methods The GenTAC Registry is a longitudinal observational cohort study enrolling patients with conditions related to genetically-induced TAAs from five regional clinical centers in the United States. Results Over 700 subjects with associated clinical histories, physical examinations, imaging data, and biospecimens have been enrolled in the Registry to date. Enrollment is expected to continue until September 2010. Total enrollment of nearly 3,000 subjects is expected. No interim analysis has yet been undertaken. Conclusions GenTAC has been established to facilitate studies by GenTAC investigators and others that will advance multiple scientific frontiers in thoracic aortic disease. Genotypic, proteomic, clinical, and imaging data will be integrated systematically with outcomes data to determine the optimal clinical management of patients suffering from genetically-induced TAAs. PMID:19185640

  4. The Generic Spacecraft Analyst Assistant (GenSAA): A tool for automating spacecraft monitoring with expert systems

    NASA Technical Reports Server (NTRS)

    Hughes, Peter M.; Luczak, Edward C.

    1991-01-01

    Flight Operations Analysts (FOAs) in the Payload Operations Control Center (POCC) are responsible for monitoring a satellite's health and safety. As satellites become more complex and data rates increase, FOAs are quickly approaching a level of information saturation. The FOAs in the spacecraft control center for the COBE (Cosmic Background Explorer) satellite are currently using a fault isolation expert system named the Communications Link Expert Assistance Resource (CLEAR), to assist in isolating and correcting communications link faults. Due to the success of CLEAR and several other systems in the control center domain, many other monitoring and fault isolation expert systems will likely be developed to support control center operations during the early 1990s. To facilitate the development of these systems, a project was initiated to develop a domain specific tool, named the Generic Spacecraft Analyst Assistant (GenSAA). GenSAA will enable spacecraft analysts to easily build simple real-time expert systems that perform spacecraft monitoring and fault isolation functions. Lessons learned during the development of several expert systems at Goddard, thereby establishing the foundation of GenSAA's objectives and offering insights in how problems may be avoided in future project, are described. This is followed by a description of the capabilities, architecture, and usage of GenSAA along with a discussion of its application to future NASA missions.

  5. Gen Green: Changes in Australian Apprentices' and Trainees' Experience of Skills and Sustainability from 2008 to 2011

    ERIC Educational Resources Information Center

    Sack, Fabian

    2012-01-01

    The Gen Green research in 2008 and 2011 indicates that skills for sustainability public policy and business initiatives are having an impact, but that young skilled Australians' high level of interest in sustainability skills is confounded by a lack of guidance and incentives from employers, the market and educators. The research indicates that,…

  6. HAMULONEMA GEN. NOV. FOR OSTERTAGIA KENYENSIS AND TELADORSAGIA HAMATA IN THE OSTERTAGIINE FAUNA (NEMATODA: TRICHOSTRONGYLOIDEA) FROM AFRICAN UNGULATES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    : Hamulonema gen. nov. is proposed for Teladorsagia hamata and Ostertagia kenyensis in the ostertagiine nematode fauna found in artiodactyl hosts from Africa. Monomorphic species representing this genus are characterized by a bilaterally symmetrical and parallel synlophe in males and females, a 2-...

  7. Evaluation of Mixed-Mode Data-Link Communications for NextGen 4DT and Equivalent Visual Surface Operations

    NASA Technical Reports Server (NTRS)

    Prinzel, Lawrence J., III; Shelton, Kevin J.; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis, J., III; Bailey, Randall E.

    2010-01-01

    By 2025, U.S. air traffic is predicted to increase 3-fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or NextGen. Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research examining data-link communications during 4DT and equivalent visual surface operations.

  8. WordGen: a tool for word selection and nonword generation in Dutch, English, German, and French.

    PubMed

    Duyck, Wouter; Desmet, Timothy; Verbeke, Lieven P C; Brysbaert, Marc

    2004-08-01

    WordGen is an easy-to-use program that uses the CELEX and Lexique lexical databases for word selection and nonword generation in Dutch, English, German, and French. Items can be generated in these four languages, specifying any combination of seven linguistic constraints: number of letters, neighborhood size, frequency, summated position-nonspecific bigram frequency, minimum position-nonspecific bigram f requency, position-specific frequency of the initial and final bigram, and orthographic relatedness. The program also has a module to calculate the respective values of these variables for items that have already been constructed, either with the program or taken from earlier studies. Stimulus queries can be entered through WordGen's graphical user interface or by means of batch files. WordGen is especially useful for (1) Dutch and German item generation, because no such stimulus-selection tool exists for these languages, (2) the generation of nonwords for all four languages, because our program has some important advantages over previous nonword generation approaches, and (3) psycholinguistic experiments on bilingualism, because the possibility of using the same tool for different languages increases the cross-linguistic comparability of the generated item lists. WordGen is free and available at http://expsy.ugent.be/wordgen.htm. PMID:15641437

  9. Bottom-up synthesis of Zn1.7GeN1.8O nanoparticles for photocatalytic application

    NASA Astrophysics Data System (ADS)

    Schliehe, Constanze; Giordano, Cristina

    2013-03-01

    Via a simple bottom-up approach, a complex quaternary oxynitride system (Zn1.7GeN1.8O) was prepared in the form of small nanoparticles (d ~ 15 nm), which were stable and morphologically well-defined. The Zn1.7GeN1.8O nanoparticles exhibited a band gap of 2.4 eV and were active towards photocatalytic degradation of organic dyes.Via a simple bottom-up approach, a complex quaternary oxynitride system (Zn1.7GeN1.8O) was prepared in the form of small nanoparticles (d ~ 15 nm), which were stable and morphologically well-defined. The Zn1.7GeN1.8O nanoparticles exhibited a band gap of 2.4 eV and were active towards photocatalytic degradation of organic dyes. Electronic supplementary information (ESI) available: SEM of the particles; absorption spectra; BET plot; TEM and XRD of the particles of the up-scaled synthesis; TEM of particles synthesized in the absence of ammonium chloride; IR-spectra; TGA plot; TEM of particles synthesized at 600 °C elemental analysis. See DOI: 10.1039/c3nr33561e

  10. Measurement of the neutron's electric form factor G(E)(n) via doubly polarized, quasi-elastic scattering at Jefferson Lab

    SciTech Connect

    Frank Wesselmann

    2004-11-01

    We determined the electric form factor of the neutron GEn via the reaction d(e,e?n)p using a longitudinally polarized electron beam and a frozen, polarized 15ND3 target at Jefferson Lab. The knocked out neutrons were detected in a segmented plastic scintillator in coincidence with the quasi-elastically scattered electrons which were tracked in Hall C's High Momentum Spectrometer. To extract GEn, we compared the experimental beam-target asymmetry with theoretical calculations based on different GEn models. We report the results of the fall 2001 run at Q2=0.5 and 1.0 (GeV/c)2.

  11. Haliea salexigens gen. nov., sp. nov., a member of the Gammaproteobacteria from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Intertaglia, Laurent; Lesongeur, Franoise; Lebaron, Philippe

    2008-05-01

    A novel aerobic, Gram-negative bacterium, designated 3X/A02/235T, was isolated from the surface of coastal waters in the north-western Mediterranean Sea. Cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 61 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria and within the family Alteromonadaceae. On the basis of 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, this isolate represents a novel species of a novel genus, for which the name Haliea salexigens gen. nov., sp. nov. is proposed. The type strain of Haliea salexigens is 3X/A02/235T (=DSM 19537T =CIP 109602T =MOLA 286T). PMID:18450719

  12. Melitea salexigens gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Agogu, Hlne; Intertaglia, Laurent; Lesongeur, Franoise; Lebaron, Philippe

    2008-11-01

    A novel aerobic, Gram-negative bacterial strain, designated 5IX/A01/131(T), was isolated from waters in the coastal north-western Mediterranean Sea. The cells were motile, straight rods, 1.6 microm long and 0.5 microm wide, and formed cream colonies on marine 2216 agar. The G+C content of the genomic DNA was 57 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparisons and physiological and biochemical characteristics, strain 5IX/A01/131(T) represents a novel genus and species, for which the name Melitea salexigens gen. nov., sp. nov. is proposed. The type strain of Melitea salexigens is 5IX/A01/131(T) (=DSM 19753(T) =CIP 109757(T) =MOLA 225(T)). PMID:18984680

  13. Coynema gen. n., a new genus of nematode (Thelastomatoidea, Hystrignathidae) parasites of Passalidae (Coleoptera) from Cuba

    PubMed Central

    Rodrguez, Jans Morffe; Rodrguez, Nayla Garca

    2011-01-01

    Abstract The new genus Coynema gen. n. is described as parasite of the two passalid beetles from Cuba: Passalus interstitialis Escholtz, 1829 (type host) and Passalus pertyi Kaup, 1869. Females are characterized by the shape of their cephalic end, cervical cuticle unarmed, a sub-cylindrical procorpus with its base abruptly dilated, fore region of intestine dilated as a sac-like structure, genital system didelphic-amphidelphic and eggs markedly ovoid and smooth-shelled. Males have a digestive system similar to females, tail sharply pointed, bearing a Y-like thickening of the dorsal cuticle. They also present a big, median, mammiform pre-cloacal papillae and a pair of small, sub-dorsal pre-cloacal papillae anterior to the cuticular thickening of the tail. PMID:21594137

  14. Multi-cusp ion source for Gen 5.5 doping system

    SciTech Connect

    Inouchi, Yutaka; Matsumoto, Takeshi; Dohi, Shojiro; Tanii, Masahiro; Takahashi, Genki; Imai, Katsuharu; Nishimura, Ippei; Tatemichi, Junichi; Konishi, Masashi; Naito, Masao

    2012-11-06

    A multi-cusp ion source was designed for Nissin ion doping system 'iG5' developed for GEN5.5 processes. It has many points of similarity to iG4 ion source. The extraction area and the internal volume of the plasma chamber are scaled up. And the method to obtain high current B{sup +} beams is same as iG4 ion source. On the other hand, iG5 ion source has an added feature on the extraction system. We use new developed multi-slit extraction system to obtain stable beams with small divergence. The target boron beam current density of 1mA/cm (that is 130mA) was obtained.

  15. Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds.

    PubMed

    Liesack, W; Bak, F; Kreft, J U; Stackebrandt, E

    1994-01-01

    A polyphasic approach was used in which genotypic and phenotypic properties of a gram-negative, obligately anaerobic, rod-shaped bacterium isolated from a black anoxic freshwater mud sample were determined. Based on these results, the name Holophaga foetida gen. nov., sp. nov. is proposed. This microorganism produced dimethylsulfide and methanethiol during growth on trimethoxybenzoate or syringate. The only other compounds utilized were pyruvate and trihydroxybenzenes such as gallate, phloroglucinol, or pyrogallol. The aromatic compounds were degraded to acetate. Although comparison of the signature nucleotide pattern of the five established subclasses of Proteobacteria with the 16S rDNA sequence of Holophaga foetida revealed a relationship to members of the delta-subclass, the phylogenetic position within the radiation of this class is so deep and dependent upon the number and selection of reference sequences that its affiliation to the Proteobacteria must be considered tentative. The type strain is H. foetida strain TMBS4 (DSM 6591). PMID:8085918

  16. SkelGen: a general tool for structure-based denovo liganddesign.

    PubMed

    Dean, Philip M; Firth-Clark, Stuart; Harris, William; Kirton, Stewart B; Todorov, Nikolay P

    2006-07-01

    The recent lapse in productivity in the pharmaceutical industry has facilitated the emergence of experimental and insilico structure-based design methodologies, based on identification of biologically active low molecular weight fragments that can be exploited to produce potential drug candidates with diverse chemistries. SkelGen, an insilico example of this methodology, is reviewed. The ability of this algorithm to identify chemically diverse low molecular weight fragments that would potentially bind to DNA gyrase is recounted, as is the first purely denovo structure-based design of five compounds that show at least micromolar activity against the estrogen receptor. The ability of the algorithm to incorporate partial protein flexibility during its design of compounds to the estrogen receptor is discussed, and an opinion as to the near and long-term futures for denovo design algorithms is expressed. PMID:23495800

  17. Eremonidiopsis aggregata, gen. n., sp. n. from Cuba, the third West Indian Dioptinae (Lepidoptera, Notodontidae)

    PubMed Central

    Aguila, Rayner Núñez

    2013-01-01

    Abstract A new genus and species of Dioptinae (Lepidoptera, Noctuoidea, Notodontidae) is described from Cuba, this being the third taxon of the subfamily known from the West Indies. Eremonidiopsis aggregata, gen. n., sp. n., appears to be closely related to Eremonidia mirifica Rawlins & Miller from Hispaniola among members of the tribe Dioptini. Eremonidiopsis aggregata is known from two localities in the middle and western portions of the northeastern Cuban mountain range, Nipe–Sagua–Baracoa. The species inhabits low elevations (300–400 m) covered by lowland rainforest and sclerophyll rainforest. The six known specimens, all males, were part of small swarms flying near the top of an unidentified tree during the day at both collecting sites. These localities are included within protected areas, the “Pico Cristal” National Park in the West and the “Alexander von Humbolt” National Park in the East. PMID:24146561

  18. Taxonomic study of a new eustigmatophycean alga, Vacuoliviride crystalliferum gen. et sp. nov.

    PubMed

    Nakayama, Takeshi; Nakamura, Atsushi; Yokoyama, Akiko; Shiratori, Takashi; Inouye, Isao; Ishida, Ken-Ichiro

    2015-03-01

    This study investigated the taxonomic affiliation of the algal strain nak-9, which has been reported to absorb radioactive cesium with high efficiency, using light and electron microscopy, and molecular phylogenetic analysis based on 18S ribosomal RNA gene (rDNA) sequences. This alga is spherical and coccoid, with a smooth cell wall, large vacuole, crystalline structure, reddish globule, and refractile granules (lamellate vesicles). The cells possess one to several greenish parietal chloroplasts with a bulging pyrenoid surrounded by lamellate vesicles. The chloroplasts include orderly thylakoid lamellae but no girdle lamella. Molecular phylogenetic analysis suggests that strain nak-9 is a member of the eustigmatophycean clade, which includes Goniochloris, Pseudostaurastrum, and Trachydiscus. On the basis of these results, we propose that strain nak-9 (NIES-2860) comprises a new species and new genus of the Eustigmatophyceae, Vacuoliviride crystalliferum gen. et sp. nov. PMID:25516501

  19. Development of Distributed Generic Simulator (GenSim) through Invention of Simulated Network (simNetwork)

    NASA Astrophysics Data System (ADS)

    Koo, Cheol-Hea; Lee, Hoon-Hee; Cheon, Yee-Jin

    2011-09-01

    A simulated network protocol provides the capability of distributed simulation to a generic simulator. Through this, full coverage of management of data and service handling among separated simulators is achieved. The distributed simulation environment is much more conducive to handling simulation load balancing and hazard treatment than a standalone computer. According to the simulated network protocol, one simulator takes on the role of server and the other simulators take on the role of client, and client is controlled by server. The purpose of the simulated network protocol is to seamlessly connect multiple simulator instances into a single simulation environment. This paper presents the development of a simulated network (simNetwork) that provides the capability of distributed simulation to a generic simulator (GenSim), which is a software simulator of satellites that has been developed by the Korea Aerospace Research Institute since 2010, to use as a flight software! validation bench for future satellite development.

  20. Reclassification of Saccharomycodes sinensis, Proposal of Yueomyces sinensis gen. nov., comb. nov. within Saccharomycetaceae (Saccharomycetales, Saccharomycotina)

    PubMed Central

    Wang, Long; Groenewald, Marizeth; Wang, Qi-Ming; Boekhout, Teun

    2015-01-01

    The phylogenetic position of Saccharomycodes sinensis has been debated by yeast taxonomists. In this study, a multigene phylogenetic analysis based on four regions, namely the 18S ribosomal DNA (rDNA), the D1/D2 domains of the 26S rDNA, the second largest subunit of RNA polymerase II gene (RPB2) and translation elongation factor 1-α gene (EF1-α), were performed to address the phylogenetic placement of S. sinensis. Our result indicated that S. sinensis belongs to Saccharomycetaceae instead of Saccharomycodaceae, and forms a single species lineage divergent from the other genera within Saccharomycetaceae. Yueomyces gen. nov. (MycoBank No. MB 811648) is proposed in the Saccharomycetaceae with Y. sinensis comb. nov. (MycoBank No. MB 811649, type strain CGMCC 2.01395T = IFO 10111T = CBS 7075T) as the type species. PMID:26375944

  1. Microstructure stability of candidate stainless steels for Gen-IV SCWR fuel cladding application

    NASA Astrophysics Data System (ADS)

    Li, Jian; Zheng, W.; Penttil, S.; Liu, P.; Woo, O. T.; Guzonas, D.

    2014-11-01

    In the past few years, significant progress has been made in materials selection for Gen-IV SCWR fuel cladding applications. Current studies indicate that austenite stainless steels such as 310H are promising candidates for in-core applications. Alloys in this group are promising for their corrosion resistance, SCC resistance, high temperature mechanical properties and creep resistance at temperatures up to 700 C. However, one under-studied area of this alloy is the long-term microstructure stability under the proposed reactor operating condition. Unstable microstructure not only results in embrittlement but also has the potential to reduce their resistance to corrosion or stress-corrosion cracking. In this study, stainless steels 310H and 304H were tested for their SCWR corrosion resistance and microstructure stability.

  2. Multimodal information Management: Evaluation of Auditory and Haptic Cues for NextGen Communication Displays

    NASA Technical Reports Server (NTRS)

    Begault, Durand R.; Bittner, Rachel M.; Anderson, Mark R.

    2012-01-01

    Auditory communication displays within the NextGen data link system may use multiple synthetic speech messages replacing traditional ATC and company communications. The design of an interface for selecting amongst multiple incoming messages can impact both performance (time to select, audit and release a message) and preference. Two design factors were evaluated: physical pressure-sensitive switches versus flat panel "virtual switches", and the presence or absence of auditory feedback from switch contact. Performance with stimuli using physical switches was 1.2 s faster than virtual switches (2.0 s vs. 3.2 s); auditory feedback provided a 0.54 s performance advantage (2.33 s vs. 2.87 s). There was no interaction between these variables. Preference data were highly correlated with performance.

  3. Investigation of strain relaxation in short-period SimGen superlattices using reciprocal space mapping

    NASA Astrophysics Data System (ADS)

    Koppensteiner, E.; Hamberger, P.; Bauer, Guenther E.; Kibbel, Horst; Presting, Hartmut; Kasper, Erich; Pesek, Andreas

    1993-11-01

    The optoelectronic properties of ultrathin SimGen strained layer superlattices (SLSs) depend strongly on their structural perfection and the strain adjustment of the SLS by a Si1-xGex alloy buffer. We used double crystal and triple axis x-ray diffractometry to characterize the structural properties of short period Si6Ge4 and Si9Ge6 SLSs grown on about 1 micrometers thick step-graded SiGe alloy buffers. As grown SLSs and samples annealed subsequently at 550 degree(s)C, 650 degree(s)C, and 780 degree(s)C for 60 min were investigated, the latter to study effects of post-growth thermal treatments typical for conventional Si device fabrication. Precise strain data were extracted from two-dimensional reciprocal space maps around (004) and (224) reciprocal lattice points. These data were used as refined input parameters for the dynamical simulation of the integrated intensity along the q[004] direction.

  4. Uktena riparia n. gen., n. sp. (Annelida, Clitellata, Lumbriculidae),a new spermatophore-producing oligochaete.

    PubMed

    Fend, Steven V; Rodriguez, Pilar; Lenat, David R

    2015-01-01

    Uktena riparia n. gen., n. sp. has been collected in hyporheic habitats at several sites in North Carolina, southeastern USA. The genus is defined by unusual characters related to reproductive structures, including the formation of encapsulated spermatophores for sperm transfer and large bundles of genital chaetae, both previously unknown in the Lumbriculidae. The simultaneous occurrence of both spermatophores and spermathecae is rare in the microdrile oligochaetes. Uktena spermatophores appear more similar to those reported in leeches than to those in other microdrile oligochaete families. Possible synapomorphies associating Uktena with the genera Kincaidiana and Guestphalinus include a filiform, ringed proboscis, a forward shift of reproductive organs relative to the usual position in the family, and spermathecae in the atrial segment. The new species adds to the already diverse, endemic lumbriculid fauna of the North Carolina Sandhills ecoregion. PMID:26250281

  5. POWER-GEN takes on upbeat feel as industry eyes end of doldrums

    SciTech Connect

    Chambers, A.

    1997-01-01

    The general atmosphere at POWER-GEN International was much more positive this year than last. It seems the industry has decided Chicken Little was wrong. Deregulation marches on, but the sky is not falling. Change is in the air, and change is never easy or comfortable, but it`s not the end of the world either. New capacity remains at a near standstill in the US as industry leaders continue to watch the nation`s reserve margins narrow, but this year talk was of the upcoming promise of construction and capacity additions instead of last year`s gloomy predictions of sweeping brown- and black-outs due to overstressed grids.

  6. A New Deep-branching Stramenopile, Platysulcus tardus gen. nov., sp. nov.

    PubMed

    Shiratori, Takashi; Nakayama, Takeshi; Ishida, Ken-ichiro

    2015-07-01

    A novel free-living heterotrophic stramenopile, Platysulcus tardus gen. nov., sp. nov. was isolated from sedimented detritus on a seaweed collected near the Ngeruktabel Island, Palau. P. tardus is a gliding flagellate with tubular mastigonemes on the anterior short flagellum and a wide, shallow ventral furrow. Although the flagellar apparatus of P. tardus is typical of stramenopiles, it shows novel ultrastructural combinations that are not applied to any groups of heterotrophic stramenopiles. Phylogenetic analysis using SSU rRNA genes revealed that P. tardus formed a clade with stramenopiles with high support. However, P. tardus did not form a subclade with any species or environmental sequences within the stramenopiles, and no close relative was suggested by the phylogenetic analysis. Therefore, we concluded that P. tardus should be treated as a new genus and species of stramenopiles and have proposed a new family, Platysulcidae fam. nov., for this phylogenetically distinct organism. PMID:26070192

  7. Combresomyces cornifer gen. sp. nov., an endophytic peronosporomycete in Lepidodendron from the Carboniferous of central France.

    PubMed

    Dotzler, Nora; Krings, Michael; Agerer, Reinhard; Galtier, Jean; Taylor, Thomas N

    2008-09-01

    Structurally preserved periderm of the lycophyte Lepidodendron rhodumnense from the Visean (Mississippian) of central France contains a peronosporomycete (Combresomyces cornifer gen. sp. nov.) that occurs in the form of pyriform to subglobose terminal oogonia. On the surface is a conspicuous ornamentation, which may have formed through condensation of a mucilaginous extra-oogonial wall secretion. Some oogonia contain thin-walled spherules, which may represent (walled) oospheres or spores of an endoparasitic fungus (?chytrid), whereas single, large spheres in the interior are interpreted as oospores. Antheridia adpressed to several of the specimens are clavate and paragynous. This discovery sheds light on the morphology and biology of peronosporomycetes in a terrestrial ecosystem some 330My ago. Although the organism occurs exclusively in the periderm of L. rhodumnense, it is not known whether it represents a symptomless endophyte, pathogen, or saprotroph. PMID:18692373

  8. NASA System-Level Design, Analysis and Simulation Tools Research on NextGen

    NASA Technical Reports Server (NTRS)

    Bardina, Jorge

    2011-01-01

    A review of the research accomplished in 2009 in the System-Level Design, Analysis and Simulation Tools (SLDAST) of the NASA's Airspace Systems Program is presented. This research thrust focuses on the integrated system-level assessment of component level innovations, concepts and technologies of the Next Generation Air Traffic System (NextGen) under research in the ASP program to enable the development of revolutionary improvements and modernization of the National Airspace System. The review includes the accomplishments on baseline research and the advancements on design studies and system-level assessment, including the cluster analysis as an annualization standard of the air traffic in the U.S. National Airspace, and the ACES-Air MIDAS integration for human-in-the-loop analyzes within the NAS air traffic simulation.

  9. Enhanced Vision for All-Weather Operations Under NextGen

    NASA Technical Reports Server (NTRS)

    Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.; Bailey, Randall E.; Kramer, Lynda J.; Williams, Steven P.

    2010-01-01

    Recent research in Synthetic/Enhanced Vision technology is analyzed with respect to existing Category II/III performance and certification guidance. The goal is to start the development of performance-based vision systems technology requirements to support future all-weather operations and the NextGen goal of Equivalent Visual Operations. This work shows that existing criteria to operate in Category III weather and visibility are not directly applicable since, unlike today, the primary reference for maneuvering the airplane is based on what the pilot sees visually through the "vision system." New criteria are consequently needed. Several possible criteria are discussed, but more importantly, the factors associated with landing system performance using automatic and manual landings are delineated.

  10. Parablastomonas arctica gen. nov., sp. nov., isolated from high Arctic glacial till.

    PubMed

    Ren, Lvzhi; Chang, Xulu; Jiang, Fan; Kan, Wenjing; Qu, Zhihao; Qiu, Xia; Fang, Chengxiang; Peng, Fang

    2015-01-01

    A pale yellow, aerobic bacterium, strain M0-2(T), was isolated from a till sample. Its taxonomic position was investigated by using a polyphasic approach. Cells were Gram-stain-negative, rod-shaped and motile. Cells reproduced by budding or asymmetrical cell division. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M0-2(T) belonged to the family Sphingomonadaceae and was closely related to species of the genera Novosphingobium (96.4-92.0%) and Blastomonas (94.6%), Sphingopyxis witflariensis W-50(T) (94.0%), Sphingosinicella soli KSL-125(T) (93.6%) and Sphingomonas astaxanthinifaciens TDMA-17(T) (93.5%). Ubiquinone-10 (Q-10) was the predominant respiratory quinone. The major fatty acids were summed feature 8 (comprising C18:1?7c and/or C18:1?6c, 31.9%), summed feature 3 (comprising C16:1?7c and/or C16:1?6c, 19.8%) and C14:0 2-OH (8.9%). Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. Spermidine was the major polyamine observed in the cell. The genomic DNA G+C content was 47.5 mol%. On the basis of phylogenetic relationships and the low DNA G+C content compared with most other genera of the family Sphingomonadaceae, combined with phenotypic and chemotaxonomic data, strain M0-2(T) is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Parablastomonas arctica gen. nov., sp. nov. is proposed. The type strain of Parablastomonas arctica gen. nov., sp. nov. is M0-2(T) (?=CCTCC AB 2012968(T)?=?NRRL B-59110(T)). PMID:25336722

  11. Application with COSI code of gen IV fast reactors introduction in the French park

    SciTech Connect

    Grouiller, Jean-Paul; Boucher, Lionel; Meyer, Maryan

    2007-07-01

    The insertion of a new concept (fuel, reactor, process) must be evaluated in the global electronuclear system with an analysis of the impact on the fuel cycle (Enrichment, Fuel Fabrication, Reactor, Processing, Interim Storage, Waste storage). An approach of scenario studies is used to evaluate different solutions to manage nuclear materials (uranium, plutonium) and wastes (minor actinides and fission products), from the present situation (partially closed cycle) until the total closed cycle with GEN IV systems, in calculating the fluxes and the inventories of these elements in each step of the fuel cycle and to treat the transient period to pass from one situation to the others. For some interesting scenarios, the approach consists on a simulation of transient scenarios from the present situation to the equilibrium situation with a COSI code. The results given at each point of the fuel cycle and for each year permit to demonstrate the technological feasibility and to evaluate the impacts on environmental, economical, proliferation and waste storage aspects. After a presentation of the operational approach, this paper gives an example for a French transient scenario between the present situation and the end of the 21. century with the introduction of GEN IV fast reactors. The results presented in this paper give the impacts on: - The natural uranium resources, - The capacity of different plants (enrichment, fabrication, reprocessing) and interim storages for spent fuels, - The inventory, function of time, of different elements (Pu, Np, Am, Cm) at each stage of the fuel cycle and in the wastes, - The thermal power the high level wastes. (authors)

  12. Pharmacogenetic Association of Hypertension Candidate Genes with Fasting Glucose in the GenHAT Study

    PubMed Central

    Irvin, Marguerite R.; Lynch, Amy I.; Kabagambe, Edmond K.; Tiwari, Hemant K.; Barzilay, Joshua I.; Eckfeldt, John H.; Boerwinkle, Eric; Davis, Barry R.; Ford, Charles E.; Arnett, Donna K.

    2010-01-01

    Several clinical studies report increased risk of diabetes mellitus (DM) with pharmacologic treatment for hypertension (HTN). HTN genes may modify glycemic response to antihypertensive treatment. The current study examined the association of 24 single nucleotide polymorphisms (SNPs) in 11 HTN candidate genes with fasting glucose measured at 2, 4, and 6 years after treatment initiation. The study sample included participants free of diabetes at baseline in the Genetics of Hypertension Associated Treatment (GenHAT) study (N=9,309). GenHAT participants were randomized to receive treatment with a diuretic (chlorthalidone), calcium channel blocker (amlodipine), or ACE inhibitor (lisinopril). Mixed models for repeated measures were employed to test for gene and pharmacogenetic associations with fasting glucose during follow-up. Fasting glucose at year 2 increased on average 6.8 mg/dL, 4.8 mg/dL and 3.0 mg/dL from baseline in the chlorthalidone, amlodipine and lisinopril groups, respectively. Carrying the I allele (rs1799752) of the angiotensin-converting enzyme (ACE) I/D polymorphism was associated with lower fasting glucose levels (P=0.02). Additionally, an ACE promoter polymorphism (?262, rs4291) was associated with lower fasting glucose for the model AA/AT vs. TT which remained significant after correction for multiple testing (P=0.001). Finally, a SNP in the ?-subunit of the amiloride-sensitive epithelial sodium channel (SCNN1A, rs2228576) modified the association of amlodipine versus chlorthalidone treatment with fasting glucose (P<0.001). Further examination of these genes and their relationships with cardiometabolic disease could foster development of pharmacogenetic guidelines aimed to prevent increases in fasting glucose during antihypertensive treatment. PMID:20577119

  13. Towards an improved modeling of chemical weathering in the SoilGen soil evolution model

    NASA Astrophysics Data System (ADS)

    Opolot, Emmanuel; Finke, Peter

    2014-05-01

    As the need for soil information particularly in the fields of agriculture, land evaluation, hydrology, biogeochemistry and climate change keeps increasing, models for soil evolution are increasingly becoming valuable tools to provide such soil information. Although still limited, such models are progressively being developed. The SoilGen model is one of such models with capabilities to provide soil information such as soil texture, pH, base saturation, organic carbon, CEC, etc over multi-millennia time scale. SoilGen is a mechanistic water flow driven pedogenetic model describing soil forming processes such as carbon cycling, clay migration, decalcification, bioturbation, physical weathering and chemical weathering. The model has been calibrated and confronted with field measurements in a number of case studies, giving plausible results. Discrepancies between measured and simulated soil properties as concluded from case studies have been mainly attributed to (i) the simple chemical weathering system (ii) poor estimates of initial data inputs such as bulk density and element fluxes, and (iii) incorrect values of variables that describe boundary conditions such as precipitation and potential evapotranspiration. This study focuses on extending the chemical weathering system, such that it can deal with a more heterogeneous composition of primary minerals and includes more elements such as Fe and Si. We propose and discuss here an extended description of chemical weathering in the model that is based on more primary minerals, taking into account the role of the specific area of these minerals, and the effect of physical weathering on these specific areas over time. In the initial stage, the proposed chemical weathering mechanism is also implemented in PHREEQC (a widely applied geochemical code with capabilities to simulate equilibrium reactions involving water and minerals, surface complexes and ion exchangers, etc.) to facilitate comparison with the model results. Results of both modeling approaches are comparable. There is however need to confront such test results with measurements.

  14. Ascidiimonas aurantiaca gen. nov., sp. nov., a member of Flavobacteriaceae isolated from a sea squirt.

    PubMed

    Yoon, Jaewoo; Oku, Naoya; Kasai, Hiroaki

    2016-04-01

    A Gram-stain negative, strictly aerobic, chemoheterotrophic, tangerine orange pigmented, curved-rod shaped bacterium, designated N5DA8-2C(T), was isolated from a sea squirt by use of a bait-streaked agar technique. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the novel marine strain is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared high (92.6 %) sequence similarity with Frondibacter aureus A5Q-67(T). The strain could be differentiated phenotypically from the related members of the family Flavobacteriaceae. The major fatty acids of strain N5DA8-2C(T) were iso-C15:1 G, iso-C17:0 3-OH, iso-C15:0 and C16:1 ω7c and/or C16:1 ω6c. A polar lipid profile was present consisting of phosphatidylethanolamine and three unidentified amino lipids. The DNA G+C content of the strain was determined to be 41 mol% and the major respiratory quinone was identified as menaquinone 6 (MK-6). From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Ascidiimonas aurantiaca gen. nov., sp. nov. is proposed. The type strain of A. aurantiaca gen. nov., sp. nov. is N5DA8-2C(T) (= KCTC 32992(T) = NBRC 110020(T)). PMID:26800666

  15. AN EXPLORATION OF DIVERSITY AMONG THE OSTERTAGIINAE: AFRICANASTRONGYLUS BUCEROS GEN. NOV. ET SP. NOV. (NEMATODA: TRICHOSTRONGYLOIDEA) IN AFRICAN BUFFALO (SYNCERUS CAFFER).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Abomasal nematodes (Ostertagiine: Trichostrongyloidea) representing a previously unrecognized genus and species are reported in African Buffalo (Syncerus caffer caffer) from Kenya, Uganda and South Africa. Africanastrongylus buceros gen. nov. et sp. nov. is characterized by a symmetrical tapering ...

  16. Clinical and radiographic evaluation of Bio-Gen with biocollagen compared with Bio-Gen with connective tissue in the treatment of class II furcation defects: a randomized clinical trial

    PubMed Central

    JENABIAN, Niloofar; HAGHANIFAR, Sina; MABOUDI, Avideh; BIJANI, Ali

    2013-01-01

    Objective Treatment of furcation defects are thought to be challenging. The purpose of this study was to evaluate the clinical and radiographic parameters of Bio-Gen with Biocollagen compared with Bio-Gen with connective tissue in the treatment of Class II furcation defects. Material and Methods In this clinical trial, 24 patients with Class II furcation defect on a buccal or lingual mandibular molar were recruited. After oral hygiene instruction, scaling and root planing and achievement of acceptable plaque control, the patients were randomly chosen to receive either connective tissue and Bio-Gen (case group) or Biocollagen and Bio-Gen (control group). The following parameters were recorded before the first and re-entry surgery (six months later): vertical clinical attachment level (VCAL), gingival index (GI), plaque index (PI), horizontal probing depth (HPD), vertical probing depth (VPD), gingival recession (GR), furcation vertical component (FVC), furcation to alveolar crest (FAC), fornix to base of defect (FBD), and furcation horizontal component (FHC) were calculated at the time of first surgery and during re-entry. A digital periapical radiograph was taken in parallel before first surgery and re-entry. The radiographs were then analyzed by digital subtraction. The differences with p value <0.05 were considered significant. Results Only the mean changes of FAC, FHC, mean of FHC, FBD in re-entry revealed statistically significant differences between the two groups. HPD, VPD, FBD, FAC, and FHC showed statistically significant differences after 6 months in the case group. However, in the control group, statistically significant differences were found in GR and HPD. We did not observe any significant difference in radiographic changes among the two groups. Conclusion The results of this trial indicate that better clinical outcomes can be obtained with connective tissue grafts in combination with bone material compared with a resorbable barrier with bone material. The differences in radiographic changes between the two groups, however, were not statistically significant. PMID:24212988

  17. Mexiare gen. nov., a new Doryctinae genus (Hymenoptera: Braconidae)from Mexico with fused first and second metasomal tergites.

    PubMed

    Belokobylskij, Sergey A; Samaca-Senz, Ernesto; Zaldvar-Rivern, Alejandro

    2015-01-01

    A new braconid genus from the subfamily Doryctinae, Mexiare gen. nov. (type species M. toledoi sp. nov.) is described from the state of Morelos in Central Mexico. The described species of this genus is characterised by having immovably fused first and second metasomal tergites, a feature also present in species of two Oriental (Arhaconotus Belokobylskij and Mimipodoryctes Belokobylskij) and one Neotropical (Iare Barbalho et Penteado-Dias) genera. The new genus, however, can be distinguished from the Neotropical Iare by the presence of a semi-oval basal area on the second metasomal tergite, distinctly short submedial (subbasal) cell of hind wing, more than three hamuli, considerably short second radiomedial (submarginal) cell, narrow radial (marginal) cell of fore wing and mostly smooth mesoscutum. A phylogenetic analysis among doryctine genera based on two gene markers (28S and COI) placed Mexiare gen. nov. within a previously recovered major South American clade, though its relationships with other taxa remain unclear. PMID:25661934

  18. Reflexión bioética sobre el uso de organismos genéticamente modificados

    PubMed Central

    Yunta, Eduardo Rodríguez

    2011-01-01

    El presente artículo reflexiona desde los 4 principios de la bioética el uso comercial de organismos genéticamente modificados. Se cuestiona fundamentalmente la falta de transferencia de tecnología entre el mundo desarrollado y en desarrollo y el que el presente sistema de patentamiento de organismos vivos modificados fomenta intereses comerciales y no da debida importancia al desarrollo sostenible de la agricultura y ganadería en los países en desarrollo, donde más se necesita. Se reflexiona sobre la importancia que tiene evaluar los riesgos antes de introducirse en el mercado organismos genéticamente modificados y la necesidad de regulación en los países. PMID:21927675

  19. Performance of the NG OligoGen kit for the diagnosis of Neisseria gonorrhoeae: comparison with cobas 4800 assay.

    PubMed

    Parra-Snchez, M; Garca-Rey, S; Marcuello, A; Zakariya-Yousef, I; Bernal, S; Pueyo, I; Martn-Mazuelos, E; Palomares, J C

    2016-01-01

    PCR assays are nowadays between the most sensitive and reliable methods for screening and diagnosing sexually transmitted infections (STIs). The aim of this study was to analyze the reliability, accuracy, and usefulness of the new NG OligoGen kit in comparison with the cobas 4800 assay for the detection of Neisseria gonorrhoeae in clinical samples. A prospective study was designed for detection of N. gonorrhoeae including urine samples (n=152), rectal (n=80), endocervical (n=67), pharyngeal (n=41), and urethral swabs (n=5) that were sent from a regional STI clinic in Seville, Spain. Samples were collected from 255 (73.9%) men and 90 women. Sensitivity, specificity, positive and negative predicative values, and kappa value for N. gonorrhoeae detection using the NG OligoGen kit were 99.6%, 100%, 100%, 99.1%, and 0.99, respectively. Statistical data obtained in this study confirm the usefulness and reliable results of this new assay. PMID:26508106

  20. Hold your horSSEs: controlling structure-selective endonucleases MUS81 and Yen1/GEN1

    PubMed Central

    Blanco, Miguel G.; Matos, Joao

    2015-01-01

    Repair of DNA lesions through homologous recombination promotes the establishment of stable chromosomal interactions. Multiple helicases, topoisomerases and structure-selective endonucleases (SSEs) act upon recombining joint molecules (JMs) to disengage chromosomal connections and safeguard chromosome segregation. Recent studies on two conserved SSEs MUS81 and Yen1/GEN1 uncovered multiple layers of regulation that operate to carefully tailor JM-processing according to specific cellular needs. Temporal restriction of SSE function imposes a hierarchy in pathway usage that ensures efficient JM-processing while minimizing reciprocal exchanges between the recombining DNAs. Whereas a conserved strategy of fine-tuning SSE functions exists in different model systems, the precise molecular mechanisms to implement it appear to be significantly different. Here, we summarize the current knowledge on the cellular switches that are in place to control MUS81 and Yen1/GEN1 functions. PMID:26284109

  1. Potamostoma shizunaiense gen. et sp. nov. (Nemertea: Hoplonemertea: Monostilifera): a new brackish-water nemertean from Japan.

    PubMed

    Kajihara, Hiroshi; Gibson, Ray; Mawatari, Shunsuke F

    2003-04-01

    Potamostoma shizunaiense gen. et sp. nov. (Nemertea: Hoplonemertea: Monostilifera) is described from the mouth of the River Shizunai, Hokkaido, Japan. This genus is readily distinguished from other monostiliferans by an oesophagus opening far anteriorly into the rhynchodaeum, a well developed excretory system extending the whole body length, terminals of the excretory collecting tubules situated between the body wall circular muscle layer and the dermis, and bilobed testes in males. PMID:12719652

  2. Surface Map Traffic Intent Displays and Net-Centric Data-link Communications for NextGen

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Prinzel, Lawrence J., III; Jones, Denise R.; Allamandola, Angela S.; Arthur, Jarvis J., III; Bailey, Randall E.

    2009-01-01

    By 2025, U.S. air traffic is predicted to increase three fold and may strain the current air traffic management system, which may not be able to accommodate this growth. In response to this challenge, a revolutionary new concept has been proposed for U.S. aviation operations, termed the Next Generation Air Transportation System or "NextGen". Many key capabilities are being identified to enable NextGen, including the use of data-link communications. Because NextGen represents a radically different approach to air traffic management and requires a dramatic shift in the tasks, roles, and responsibilities for the flight deck, there are numerous research issues and challenges that must be overcome to ensure a safe, sustainable air transportation system. Flight deck display and crew-vehicle interaction concepts are being developed that proactively investigate and overcome potential technology and safety barriers that might otherwise constrain the full realization of NextGen. The paper describes simulation research, conducted at National Aeronautics and Space Administration (NASA) Langley Research Center, examining data-link communications and traffic intent data during envisioned four-dimensional trajectory (4DT)-based and equivalent visual (EV) surface operations. Overall, the results suggest that controller pilot data-link communications (CPDLC) with the use of mandatory pilot read-back of all clearances significantly enhanced situation awareness for 4DT and EV surface operations. The depiction of graphical traffic state and intent information on the surface map display further enhanced off-nominal detection and pilot qualitative reports of safety and awareness.

  3. Quisarctus yasumurai gen. et sp. nov. (Arthrotardigrada: Halechiniscidae)from a submarine cave, off Iejima, Ryukyu Islands, Japan.

    PubMed

    Fujimoto, Shinta

    2015-01-01

    Quisarctus yasumurai gen. et sp. nov. (Arthrotardigrada: Halechiniscidae) is described from the submarine cave 'Daidokutsu', off Iejima, Okinawa Islands, Ryukyu Islands, Japan. It is characterised by a cylindrical body, long primary clava and shorter lateral cirrus inserted on a common cirrophore, and simple digits of unequal lengths (without folds, peduncles, proximal pads, pretarsi, or wrinkles) that terminate in a sheathed, small, crescent-shaped claw with a minute calcar. Quisarctinae subfam. nov. is erected for this unique new genus. PMID:25947769

  4. Genome Sequences of Oblitimonas alkaliphila gen. nov. sp. nov. (Proposed), a Novel Bacterium of the Pseudomonadaceae Family

    PubMed Central

    Lauer, Ana C.; Humrighouse, Ben W.; Emery, Brian; Drobish, Adam; Juieng, Phalasy; Loparev, Vladimir; McQuiston, John R.

    2015-01-01

    Results obtained through 16S rRNA gene sequencing and phenotypic testing of eight related, but unidentified, isolates located in a historical collection at the Centers for Disease Control and Prevention suggested that these isolates belong to a novel genera of bacteria. The genomes of the bacteria, to be named Oblitimonas alkaphilia gen. nov. sp. nov., were sequenced using Illumina technology. Closed genomes were produced for all eight isolates. PMID:26679585

  5. Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

    PubMed Central

    2008-01-01

    Background The lack of reference sequences from well-identified mycorrhizal fungi often poses a challenge to the inference of taxonomic affiliation of sequences from environmental samples, and many environmental sequences are thus left unidentified. Such unidentified sequences belonging to the widely distributed ectomycorrhizal fungal genus Inocybe (Basidiomycota) were retrieved from GenBank and divided into species that were identified in a phylogenetic context using a reference dataset from an ongoing study of the genus. The sequence metadata of the unidentified Inocybe sequences stored in GenBank, as well as data from the corresponding original papers, were compiled and used to explore the ecology and distribution of the genus. In addition, the relative occurrence of Inocybe was contrasted to that of other mycorrhizal genera. Results Most species of Inocybe were found to have less than 3% intraspecific variability in the ITS2 region of the nuclear ribosomal DNA. This cut-off value was used jointly with phylogenetic analysis to delimit and identify unidentified Inocybe sequences to species level. A total of 177 unidentified Inocybe ITS sequences corresponding to 98 species were recovered, 32% of which were successfully identified to species level in this study. These sequences account for an unexpectedly large proportion of the publicly available unidentified fungal ITS sequences when compared with other mycorrhizal genera. Eight Inocybe species were reported from multiple hosts and some even from hosts forming arbutoid or orchid mycorrhizae. Furthermore, Inocybe sequences have been reported from four continents and in climate zones ranging from cold temperate to equatorial climate. Out of the 19 species found in more than one study, six were found in both Europe and North America and one was found in both Europe and Japan, indicating that at least many north temperate species have a wide distribution. Conclusion Although DNA-based species identification and circumscription are associated with practical and conceptual difficulties, they also offer new possibilities and avenues for research. Metadata assembly holds great potential to synthesize valuable information from community studies for use in a species and taxonomy-oriented framework. PMID:18282272

  6. The Populus Genome Integrative Explorer (PopGenIE): a new resource for exploring the Populus genome.

    PubMed

    Sjdin, Andreas; Street, Nathaniel Robert; Sandberg, Gran; Gustafsson, Petter; Jansson, Stefan

    2009-06-01

    Populus has become an important model plant system. However, utilization of the increasingly extensive collection of genetics and genomics data created by the community is currently hindered by the lack of a central resource, such as a model organism database (MOD). Such MODs offer a single entry point to the collection of resources available within a model system, typically including tools for exploring and querying those resources. As a starting point to overcoming the lack of such an MOD for Populus, we present the Populus Genome Integrative Explorer (PopGenIE), an integrated set of tools for exploring the Populus genome and transcriptome. The resource includes genome, synteny and quantitative trait locus (QTL) browsers for exploring genetic data. Expression tools include an electronic fluorescent pictograph (eFP) browser, expression profile plots, co-regulation within collated transcriptomics data sets, and identification of over-represented functional categories and genomic hotspot locations. A number of collated transcriptomics data sets are made available in the eFP browser to facilitate functional exploration of gene function. Additional homology and data extraction tools are provided. PopGenIE significantly increases accessibility to Populus genomics resources and allows exploration of transcriptomics data without the need to learn or understand complex statistical analysis methods. PopGenIE is available at www.popgenie.org or via www.populusgenome.info. PMID:19383103

  7. Meeting Air Transportation Demand in 2025 by Using Larger Aircraft and Alternative Routing to Complement NextGen Operational Improvements

    NASA Technical Reports Server (NTRS)

    Smith, Jeremy C.; Guerreiro, Nelson M.; Viken, Jeffrey K.; Dollyhigh, Samuel M.; Fenbert, James W.

    2010-01-01

    A study was performed that investigates the use of larger aircraft and alternative routing to complement the capacity benefits expected from the Next Generation Air Transportation System (NextGen) in 2025. National Airspace System (NAS) delays for the 2025 demand projected by the Transportation Systems Analysis Models (TSAM) were assessed using NASA s Airspace Concept Evaluation System (ACES). The shift in demand from commercial airline to automobile and from one airline route to another was investigated by adding the route delays determined from the ACES simulation to the travel times used in the TSAM and re-generating new flight scenarios. The ACES simulation results from this study determined that NextGen Operational Improvements alone do not provide sufficient airport capacity to meet the projected demand for passenger air travel in 2025 without significant system delays. Using larger aircraft with more seats on high-demand routes and introducing new direct routes, where demand warrants, significantly reduces delays, complementing NextGen improvements. Another significant finding of this study is that the adaptive behavior of passengers to avoid congested airline-routes is an important factor when projecting demand for transportation systems. Passengers will choose an alternative mode of transportation or alternative airline routes to avoid congested routes, thereby reducing delays to acceptable levels for the 2025 scenario; the penalty being that alternative routes and the option to drive increases overall trip time by 0.4% and may be less convenient than the first-choice route.

  8. Hardware and Software Design of FPGA-based PCIe Gen3 interface for APEnet+ network interconnect system

    NASA Astrophysics Data System (ADS)

    Ammendola, R.; Biagioni, A.; Frezza, O.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Paolucci, P. S.; Pastorelli, E.; Rossetti, D.; Simula, F.; Tosoratto, L.; Vicini, P.

    2015-12-01

    In the attempt to develop an interconnection architecture optimized for hybrid HPC systems dedicated to scientific computing, we designed APEnet+, a point-to-point, low-latency and high-performance network controller supporting 6 fully bidirectional off-board links over a 3D torus topology. The first release of APEnet+ (named V4) was a board based on a 40 nm Altera FPGA, integrating 6 channels at 34 Gbps of raw bandwidth per direction and a PCIe Gen2 x8 host interface. It has been the first-of-its-kind device to implement an RDMA protocol to directly read/write data from/to Fermi and Kepler NVIDIA GPUs using NVIDIA peer-to-peer and GPUDirect RDMA protocols, obtaining real zero-copy GPU-to-GPU transfers over the network. The latest generation of APEnet+ systems (now named V5) implements a PCIe Gen3 x8 host interface on a 28 nm Altera Stratix V FPGA, with multi-standard fast transceivers (up to 14.4 Gbps) and an increased amount of configurable internal resources and hardware IP cores to support main interconnection standard protocols. Herein we present the APEnet+ V5 architecture, the status of its hardware and its system software design. Both its Linux Device Driver and the low-level libraries have been redeveloped to support the PCIe Gen3 protocol, introducing optimizations and solutions based on hardware/software co-design.

  9. Mudwigglus gen. n. (Nematoda: Diplopeltidae) from the continental slope of New Zealand, with description of three new species and notes on their distribution.

    PubMed

    Leduc, Daniel

    2013-01-01

    Three new free-living nematode species belonging to the genus Mudwigglus gen. n. are described from the continental slope of New Zealand. The new genus is characterised by four short cephalic setae, fovea amphidialis in the shape of an elongated loop, narrow mouth opening, small, lightly cuticularised buccal cavity, pharynx with oval-shaped basal bulb, and secretory-excretory pore (if present) at level of pharyngeal bulb or slightly anterior. Mudwigglus gen. et sp. n. differs from other genera of the family Diplopeltidae in the combination of the following traits: presence of reflexed ovaries, male reproductive system with both testes directed anteriorly and reflexed posterior testis, and presence of tubular pre-cloacal supplements and pre-cloacal seta. Mudwigglus patumuka gen. et sp. n. is characterised by gubernaculum with dorso-caudal apophyses, vagina directed posteriorly, and short conical tail with three terminal setae. M. macramphidum gen. et sp. n. is characterised by long fovea amphidialis, cylindrical buccal cavity, gubernaculum without apophyses, vagina at right angle to body surface, and conico-cylindrical tail without terminal setae. M. plebeius gen. et sp. n. is characterised by cylindrical buccal cavity with cuticularised ring, gubernaculum with dorso-caudal apophyses, females with vagina directed posteriorly, and conico-cylindrical tail with two terminal setae. Diplopeluta nellyae Vinex and Gourbault, 1992 is transferred to Mudwigglus gen. n. based on observations of paratypes from New Caledonia, and of specimens from the New Zealand continental slope, which both show the presence of two testes facing anteriorly. M. macramphidum gen. et sp. n. was restricted to a single site on Chatham Rise crest (350 m water depth), whereas M. patumuka gen. et sp. was recorded from six sites on western Chatham Rise (350-2800 m). M. plebeius gen. et sp. n. was recorded from 13 sites on Chatham Rise and two sites on Challenger Plateau (264-2300 m). Mudwigglus nellyae comb. n. was restricted to two Challenger Plateau sites. All Mudwigglus gen. n. species appear to be restricted to subsurface sediments. PMID:25243291

  10. GenSo-EWS: a novel neural-fuzzy based early warning system for predicting bank failures.

    PubMed

    Tung, W L; Quek, C; Cheng, P

    2004-05-01

    Bank failure prediction is an important issue for the regulators of the banking industries. The collapse and failure of a bank could trigger an adverse financial repercussion and generate negative impacts such as a massive bail out cost for the failing bank and loss of confidence from the investors and depositors. Very often, bank failures are due to financial distress. Hence, it is desirable to have an early warning system (EWS) that identifies potential bank failure or high-risk banks through the traits of financial distress. Various traditional statistical models have been employed to study bank failures [J Finance 1 (1975) 21; J Banking Finance 1 (1977) 249; J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073]. However, these models do not have the capability to identify the characteristics of financial distress and thus function as black boxes. This paper proposes the use of a new neural fuzzy system [Foundations of neuro-fuzzy systems, 1997], namely the Generic Self-organising Fuzzy Neural Network (GenSoFNN) [IEEE Trans Neural Networks 13 (2002c) 1075] based on the compositional rule of inference (CRI) [Commun ACM 37 (1975) 77], as an alternative to predict banking failure. The CRI based GenSoFNN neural fuzzy network, henceforth denoted as GenSoFNN-CRI(S), functions as an EWS and is able to identify the inherent traits of financial distress based on financial covariates (features) derived from publicly available financial statements. The interaction between the selected features is captured in the form of highly intuitive IF-THEN fuzzy rules. Such easily comprehensible rules provide insights into the possible characteristics of financial distress and form the knowledge base for a highly desired EWS that aids bank regulation. The performance of the GenSoFNN-CRI(S) network is subsequently benchmarked against that of the Cox's proportional hazards model [J Banking Finance 10 (1986) 511; J Banking Finance 19 (1995) 1073], the multi-layered perceptron (MLP) and the modified cerebellar model articulation controller (MCMAC) [IEEE Trans Syst Man Cybern: Part B 30 (2000) 491] in predicting bank failures based on a population of 3635 US banks observed over a 21 years period. Three sets of experiments are performed-bank failure classification based on the last available financial record and prediction using financial records one and two years prior to the last available financial statements. The performance of the GenSoFNN-CRI(S) network as a bank failure classification and EWS is encouraging. PMID:15109685

  11. Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost.

    PubMed

    Kim, Soo-Jin; Tamura, Tomohiko; Hamada, Moriyuki; Ahn, Jae-Hyung; Weon, Hang-Yeon; Park, In-Cheol; Suzuki, Ken-Ichiro; Kwon, Soon-Wo

    2012-10-01

    A Gram-positive, aerobic, non-motile, short rod, designated SMC46(T), was isolated from a spent mushroom compost sample collected in the Suwon region, South Korea. 16S rRNA gene sequence analysis revealed that strain SMC46(T) was a member of the family Microbacteriaceae; however, the isolate formed a branch separate from other genera within the family. Sequence similarity between strain SMC46(T) and other members of the family Microbacteriaceae was ?97?%, the highest sequence similarity being with Frigoribacterium faeni 801(T) and Frondihabitans australicus E1HC-02(T) (both 97.0?%). Some chemotaxonomic properties of strain SMC46(T) were consistent with those of the family Microbacteriaceae: MK-11 and MK-12 as the predominant menaquinones, anteiso-C(15?:?0), iso-C(16?:?0) and anteiso-C(17?:?0) as the major cellular fatty acids and diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid as the polar lipids. However, strain SMC46(T) contained a B-type peptidoglycan not previously found in the family Microbacteriaceae. The DNA G+C content was 68 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain SMC46(T) was considered to represent a novel genus and species in the family Microbacteriaceae, for which the name Compostimonas suwonensis gen. nov., sp. nov. is proposed. The type strain of the type species is SMC46(T) (?=?KACC 13354(T) ?=?NBRC 106304(T)). PMID:22140170

  12. Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses.

    PubMed

    da Silva Malone, Camila Francieli; Rigonato, Janana; Laughinghouse, Haywood Dail; Schmidt, der Carlos; Bouzon, Zenilda Laurita; Wilmotte, Annick; Fiore, Marli Ftima; Sant'Anna, Clia Leite

    2015-09-01

    For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus analyses). Using a multifaceted approach, we propose a new, well-defined genus, Cephalothrix gen. nov., by analysing seven filamentous strains that are morphologically 'intermediate' between gas-vacuolated taxa and Phormidium. Furthermore, we characterize two novel species: Cephalothrix komarekiana sp. nov. (strains CCIBt 3277, CCIBt 3279, CCIBt 3523, CCALA 155, SAG 75.79 and UTEX 1580) and Cephalothrix lacustris sp. nov. (strain CCIBt 3261). The generic name and specific epithets are proposed under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants. PMID:26031295

  13. Investigating contact toxicity of Geranium and Artemisia essential oils on Bemisia tabaci Gen.

    PubMed Central

    Yarahmadi, Fatemeh; Rajabpour, Ali; Zandi Sohani, Nooshin; Ramezani, Leila

    2013-01-01

    Objective: Sweet potato whitefly, Bemisia tabaci Gen. (B. tabaci), is one of the most important pests of various greenhouse crops in Iran. Nowadays, chemical insecticides are broadly used for control of the pests that causes risk to consumer's health. For the first time, contact toxicity of Pelargonium roseum Andrews and Artemisia sieberi Besser essential oils on B. tabaci and its possible application against the whitefly was evaluated in 2012. Materials and Methods: Essential oil with concentrations of 2500, 1250, 125, and 12 ppm were used. Infested leaves of greenhouse cucumber were treated by mentioned concentrations. After 24 hours, mortality of B. tabaci was recorded and compared after correcting by Abbot's formula. Results: Results showed that all concentrations of the essential oil could significantly reduce population of B. tabaci compared with the control treatment. Phytotoxicity of the treated leaves were recorded after 24, 48, and 72 hours and compared with the control. Concentrations of 2500, 1250, and 125 ppm caused severe phytotoxicity on greenhouse cucumber leaves and therefore are not suitable for greenhouse application. Phytotoxicity of 12 ppm was relatively low. Conclusions: This data implicated suitable protective effects of the essential oils to the pest infestation. Therefore, essential oils distillated from Geranium and Artemisia could be applied to control B. tabaci in greenhouse cucumber at V/V 12 ppm. PMID:25050264

  14. Eionea nigra gen. nov., sp. nov., a gammaproteobacterium from the Mediterranean Sea.

    PubMed

    Urios, Laurent; Intertaglia, Laurent; Lesongeur, Franoise; Lebaron, Philippe

    2011-07-01

    A novel aerobic, gram-negative bacterial strain, designated 17X/A02/237(T), was isolated from waters of the coastal north-western Mediterranean Sea. Cells were motile straight rods and formed dark-grey colonies on marine agar medium. Strain 17X/A02/237(T) contained ubiquinone Q-8 and its major fatty acids were C(16?:?1)?7c and/or iso-C(15?:?0) 2-OH, C(18?:?1)?7c, C(16?:?0), C(18?:?0) and C(10?:?0) 3-OH. The G+C content of the genomic DNA was 47.5 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the class Gammaproteobacteria. Based on 16S rRNA gene sequence data, as well as physiological and biochemical characteristics, this isolate represents a novel species of a new genus, for which the name of Eionea nigra gen. nov., sp. nov. is proposed. The type strain is 17X/A02/237(T) (?=?DSM 19752(T)?=?CIP 109759(T)?=?MOLA 288(T)). PMID:20729310

  15. Hapsidoxylon terpsichorum gen. et sp. nov., a stem with unusual anatomy from the Triassic of Antarctica.

    PubMed

    McManus, Hilary A; Boucher, Lisa; Taylor, Edith L; Taylor, Thomas N

    2002-12-01

    The Middle Triassic flora of the Fremouw Formation in the central Transantarctic Mountains consists of conifers, cycads, ferns, pteridosperms, and sphenophytes. Stems with an unusual anatomy have been discovered within silicified peat from the same locality. The diameters of the stems range from 1.4 to 1.7 cm; the longest specimen is approximately 12 cm. In transverse section the vascular system consists of segments that occur as single traces or are connected in the center and anastomose at varying levels within the stem. Each segment contains a bifacial vascular cambium. Secondary tissues of each segment surround a central area of parenchyma and small tracheids presumed to represent primary xylem. Surrounding the stem is a periderm. Traces are produced near the periphery of the axis and consist of radially arranged secondary xylem and a thick periderm. The absence of leaves and reproductive organs leads to uncertain phylogenetic relationships. We are unaware of any Triassic plants with this type of vascular tissue organization, and those plants with a similar type of arrangement occur only in the Devonian and Carboniferous. Possible phylogenetic affinities with the Cladoxylales and Lycophyta are examined, but the anatomical differences, along with stratigraphic age, preclude formal assignment to any known taxon at this time. Therefore, we have assigned it to a new taxon: Hapsidoxylon terpsichorum gen. et sp. nov. PMID:21665624

  16. Molecular and morphological characterization of Veleshkinema iranicum n. gen., n. sp. (Nematoda: Hexatylina, Sphaerularioidea) from Iran.

    PubMed

    Miraeiz, Esmaeil; Heydari, Ramin; lvarez-Ortega, Sergio; Pedram, Majid; Atighi, Mohammad Reza

    2015-01-01

    Veleshkinema iranicum n. gen., n. sp. is described and illustrated based on morphological, morphometric and molecular characters. The new genus is characterized by having slender females and males, stylet with asymmetrical knobs, dorsal gland orifice just posterior to subventral knob, lip region with flattened apex and eight sectors, pharynx with a non-muscular and non-valvular median bulb, pharyngeal glands slightly overlapping intestine dorsally, visible cellular cardia, female with a single gonad having a quadricolumellate crustaformeria with 8-10 cells in each column, no postvulval uterine sac and rounded and offset spermatheca containing spheroid sperm cells, males with arcuate tylenchoid spicules and subterminal bursa. The new genus is morphologically compared with four genera: Abursanema, Deladenus, Prothallonema and Sphaerularia. Molecular phylogenetic studies of the new genus using 808 bp partial sequences of SSU ribosomal RNA gene placed the new genus in a clade with Sphaerularia spp. In phylogenetic analyses using 756 bp partial sequences of the 28S ribosomal RNA gene (D2-D3 segments), the new genus formed a monophyletic group with Abursanema iranicum and Sphaerularia spp. PMID:26623744

  17. Bandoniozyma gen. nov., a Genus of Fermentative and Non-Fermentative Tremellaceous Yeast Species

    PubMed Central

    Landell, Melissa Fontes; Crestani, Juliana; Pagnocca, Fernando Carlos; Sette, Lara Dures; Passarini, Michel Rodrigo Zambrano; Rosa, Carlos Augusto; Brando, Luciana R.; Pimenta, Raphael S.; Ribeiro, Jos Roberto; Garcia, Karina Marques; Lee, Ching-Fu; Suh, Sung-Oui; Pter, Gbor; Dlauchy, Dnes; Fell, Jack W.; Scorzetti, Gloria; Theelen, Bart; Vainstein, Marilene H.

    2012-01-01

    Background Independent surveys across the globe led to the proposal of a new basidiomycetous yeast genus within the Bulleromyces clade of the Tremellales, Bandoniozyma gen. nov., with seven new species. Methodology/Principal Findings The species were characterized by multiple methods, including the analysis of D1/D2 and ITS nucleotide sequences, and morphological and physiological/biochemical traits. Most species can ferment glucose, which is an unusual trait among basidiomycetous yeasts. Conclusions/Significance In this study we propose the new yeast genus Bandoniozyma, with seven species Bandoniozyma noutii sp. nov. (type species of genus; CBS 8364T ?=? DBVPG 4489T), Bandoniozyma aquatica sp. nov. (UFMG-DH4.20T ?=? CBS 12527T ?=? ATCC MYA-4876T), Bandoniozyma complexa sp. nov. (CBS 11570T ?=? ATCC MYA-4603T ?=? MA28aT), Bandoniozyma fermentans sp. nov. (CBS 12399T ?=? NU7M71T ?=? BCRC 23267T), Bandoniozyma glucofermentans sp. nov. (CBS 10381T ?=? NRRL Y-48076T ?=? ATCC MYA-4760T ?=? BG 02-7-15-015A-1-1T), Bandoniozyma tunnelae sp. nov. (CBS 8024T ?=? DBVPG 7000T), and Bandoniozyma visegradensis sp. nov. (CBS 12505T ?=? NRRL Y-48783T ?=? NCAIM Y.01952T). PMID:23056233

  18. Kretzoiarctos gen. nov., the Oldest Member of the Giant Panda Clade

    PubMed Central

    Abella, Juan; Alba, David M.; Robles, Josep M.; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Raül; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8–7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12–11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

  19. Using Game Theoretic Models to Predict Pilot Behavior in NextGen Merging and Landing Scenario

    NASA Technical Reports Server (NTRS)

    Yildiz, Yildiray; Lee, Ritchie; Brat, Guillaume

    2012-01-01

    In this paper, we present an implementation of the Semi Network-Form Game framework to predict pilot behavior in a merging and landing scenario. In this scenario, two aircraft are approaching to a freeze horizon with approximately equal distance when they become aware of each other via an ADS-B communication link that will be available in NextGen airspace. Both pilots want to gain advantage over the other by entering the freeze horizon earlier and obtain the first place in landing. They re-adjust their speed accordingly. However, they cannot simply increase their speed to the maximum allowable values since they are concerned with safety, separation distance, effort, possibility of being vectored-off from landing and possibility of violating speed constraints. We present how to model these concerns and the rest of the system using semi network-from game framework. Using this framework, based on certain assumptions on pilot utility functions and on system configuration, we provide estimates of pilot behavior and overall system evolution in time. We also discuss the possible employment of this modeling tool for airspace design optimization. To support this discussion, we provide a case where we investigate the effect of increasing the merging point speed limit on the commanded speed distribution and on the percentage of vectored aircraft.

  20. GenInfoGuard--a robust and distortion-free watermarking technique for genetic data.

    PubMed

    Iftikhar, Saman; Khan, Sharifullah; Anwar, Zahid; Kamran, Muhammad

    2015-01-01

    Genetic data, in digital format, is used in different biological phenomena such as DNA translation, mRNA transcription and protein synthesis. The accuracy of these biological phenomena depend on genetic codes and all subsequent processes. To computerize the biological procedures, different domain experts are provided with the authorized access of the genetic codes; as a consequence, the ownership protection of such data is inevitable. For this purpose, watermarks serve as the proof of ownership of data. While protecting data, embedded hidden messages (watermarks) influence the genetic data; therefore, the accurate execution of the relevant processes and the overall result becomes questionable. Most of the DNA based watermarking techniques modify the genetic data and are therefore vulnerable to information loss. Distortion-free techniques make sure that no modifications occur during watermarking; however, they are fragile to malicious attacks and therefore cannot be used for ownership protection (particularly, in presence of a threat model). Therefore, there is a need for a technique that must be robust and should also prevent unwanted modifications. In this spirit, a watermarking technique with aforementioned characteristics has been proposed in this paper. The proposed technique makes sure that: (i) the ownership rights are protected by means of a robust watermark; and (ii) the integrity of genetic data is preserved. The proposed technique-GenInfoGuard-ensures its robustness through the "watermark encoding" in permuted values, and exhibits high decoding accuracy against various malicious attacks. PMID:25689741

  1. Antricoccus suffuscus gen. nov., sp. nov., isolated from a natural cave.

    PubMed

    Lee, Soon Dong

    2015-12-01

    A novel actinobacterium, designated strain C4-31T, was isolated from soil collected from a cave. Cells were aerobic, Gram-reaction-positive, oxidase-negative, catalase-positive and non-motile cocci. Comparison of 16S rRNA gene sequences showed that the organism occupied a distinct phylogenetic position within the suborder Frankineae, with sequence similarity values of less than 93.2?% to members of this suborder. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unknown aminophospholipid and an unknown phospholipid. The major fatty acids were iso-C16?:?0, C17?:?1?6c and C16?:?0. The G+C content of the DNA was 62.8?mol%. On the basis of morphological and chemotaxonomic data as well as phylogenetic evidence, strain C4-31T (?=?KCTC 39556T?=?DSM 100065T) is considered to represent the type strain of a novel species of a new genus in the suborder Frankineae, for which the name Antricoccus suffuscus gen. nov., sp. nov. is proposed. PMID:26358117

  2. [The quantitative testing of V617F mutation in gen JAK2 using pyrosequencing technique].

    PubMed

    Dunaeva, E A; Mironov, K O; Dribnokhodova, T E; Subbotina, E E; Bashmakova; Ol'hovski?, I A; Shipulin, G A

    2014-11-01

    The somatic mutation V617F in gen JAK2 is a frequent cause of chronic myeloprolific diseases not conditioned by BCR/ABL mutation. The quantitative testing of relative percentage of mutant allele can be used in establishing severity of disease and its prognosis and in prescription of remedy inhibiting activity of JAK2. To quantitatively test mutation the pyrosequencing technique was applied. The developed technique permits detecting and quantitatively, testing percentage of mutation fraction since 7%. The "gray zone" is presented by samples with percentage of mutant allele from 4% to 7%. The dependence of expected percentage of mutant fraction in analyzed sample from observed value of signal is described by equation of line with regression coefficients y = - 0.97, x = -1.32 and at that measurement uncertainty consists 0.7. The developed technique is approved officially on clinical material from 192 patients with main forms of myeloprolific diseases not conditioned by BCR/ABL mutation. It was detected 64 samples with mautant fraction percentage from 13% to 91%. The developed technique permits implementing monitoring of therapy of myeloprolific diseases and facilitates to optimize tactics of treatment. PMID:25850251

  3. Kretzoiarctos gen. nov., the oldest member of the giant panda clade.

    PubMed

    Abella, Juan; Alba, David M; Robles, Josep M; Valenciano, Alberto; Rotgers, Cheyenn; Carmona, Ral; Montoya, Plinio; Morales, Jorge

    2012-01-01

    The phylogenetic position of the giant panda, Ailuropoda melanoleuca (Carnivora: Ursidae: Ailuropodinae), has been one of the most hotly debated topics by mammalian biologists and paleontologists during the last century. Based on molecular data, it is currently recognized as a true ursid, sister-taxon of the remaining extant bears, from which it would have diverged by the Early Miocene. However, from a paleobiogeographic and chronological perspective, the origin of the giant panda lineage has remained elusive due to the scarcity of the available Miocene fossil record. Until recently, the genus Ailurarctos from the Late Miocene of China (ca. 8-7 mya) was recognized as the oldest undoubted member of the Ailuropodinae, suggesting that the panda lineage might have originated from an Ursavus ancestor. The role of the purported ailuropodine Agriarctos, from the Miocene of Europe, in the origins of this clade has been generally dismissed due to the paucity of the available material. Here, we describe a new ailuropodine genus, Kretzoiarctos gen. nov., based on remains from two Middle Miocene (ca. 12-11 Ma) Spanish localities. A cladistic analysis of fossil and extant members of the Ursoidea confirms the inclusion of the new genus into the Ailuropodinae. Moreover, Kretzoiarctos precedes in time the previously-known, Late Miocene members of the giant panda clade from Eurasia (Agriarctos and Ailurarctos). The former can be therefore considered the oldest recorded member of the giant panda lineage, which has significant implications for understanding the origins of this clade from a paleobiogeographic viewpoint. PMID:23155439

  4. Neoceratium gen. nov., a new genus for all marine species currently assigned to Ceratium (Dinophyceae).

    PubMed

    Gmez, Fernando; Moreira, David; Lpez-Garca, Purificacin

    2010-01-01

    The dinoflagellate genus Ceratium contains marine and freshwater species. Freshwater species possess six cingular plates, thick plates in the concave ventral area and usually develop a third hypothecal horn. The marine Ceratium species (>62 species) possess five cingular plates and thin plates in the concave ventral area; a third hypothecal horn is atypical. Resting cysts, a common feature in the freshwater species, are unreported in marine species. We illustrate for the first time resting cysts in marine Ceratium species (C. furca and C. candelabrum). We obtained small subunit ribosomal RNA gene (SSU rDNA) sequences of 23 Ceratium species (more than one third of the total marine species described so far), with representatives of the four acknowledged subgenera. Phylogenetic analyses including the type species, the freshwater C. hirundinella, showed that the four available sequences of freshwater species formed a strongly supported subclade, very distant from the marine cluster. Our data support the splitting of Ceratium sensu lato into two genera. Ceratium sensu stricto should be reserved for freshwater species possessing six cingular plates (three cingular plates in dorsal view). The new genus name, Neoceratium gen. nov. should be applied to the marine species of Ceratium sensu lato that possess five cingular plates (two cingular plates in dorsal view). PMID:19665427

  5. Development of Complexity Science and Technology Tools for NextGen Airspace Research and Applications

    NASA Technical Reports Server (NTRS)

    Holmes, Bruce J.; Sawhill, Bruce K.; Herriot, James; Seehart, Ken; Zellweger, Dres; Shay, Rick

    2012-01-01

    The objective of this research by NextGen AeroSciences, LLC is twofold: 1) to deliver an initial "toolbox" of algorithms, agent-based structures, and method descriptions for introducing trajectory agency as a methodology for simulating and analyzing airspace states, including bulk properties of large numbers of heterogeneous 4D aircraft trajectories in a test airspace -- while maintaining or increasing system safety; and 2) to use these tools in a test airspace to identify possible phase transition structure to predict when an airspace will approach the limits of its capacity. These 4D trajectories continuously replan their paths in the presence of noise and uncertainty while optimizing performance measures and performing conflict detection and resolution. In this approach, trajectories are represented as extended objects endowed with pseudopotential, maintaining time and fuel-efficient paths by bending just enough to accommodate separation while remaining inside of performance envelopes. This trajectory-centric approach differs from previous aircraft-centric distributed approaches to deconfliction. The results of this project are the following: 1) we delivered a toolbox of algorithms, agent-based structures and method descriptions as pseudocode; and 2) we corroborated the existence of phase transition structure in simulation with the addition of "early warning" detected prior to "full" airspace. This research suggests that airspace "fullness" can be anticipated and remedied before the airspace becomes unsafe.

  6. Arhodomonas aquaeolei gen. nov., sp. nov., an aerobic, halophilic bacterium isolated from a subterranean brine.

    PubMed

    Adkins, J P; Madigan, M T; Mandelco, L; Woese, C R; Tanner, R S

    1993-07-01

    Arhodomonas aquaeolei gen. nov., sp. nov., isolated from a petroleum reservoir production fluid, is described. The single isolate was an obligately halophilic, aerobic, gram-negative, oval rod-shaped bacterium that was actively motile by means of a single polar flagellum. It was catalase and oxidase positive. The isolate had a specific requirement for NaCl; growth occurred at NaCl concentrations between 6 and 20%, and optimal growth occurred in the presence of 15% NaCl. This species metabolized primarily organic acids and required biotin for growth. The name Arhodomonas is proposed for the new genus, which was placed in the gamma subclass of the Proteobacteria on the basis of the results of a 16S rRNA sequence analysis. Although A. aquaeolei is most closely related to purple sulfur bacteria (the genera Ectothiorhodospira and Chromatium), it is not a phototrophic microorganism, which is consistent with its isolation from a subterranean environment. The major components of its cellular fatty acids were C16:0, C18:1, C19:0, C16:1, and C18:0 acids. The DNA base composition of the type strain is 67 mol% G+C. The type and only strain is strain HA-1 (= ATCC 49307). PMID:8347510

  7. Isolation and classification of a novel marine Bacteroidetes as Frondibacter aureus gen. nov., sp. nov.

    PubMed

    Yoon, Jaewoo; Adachi, Kyoko; Kasai, Hiroaki

    2015-02-01

    A facultatively anaerobic, Gram-stain negative, golden-yellow pigmented, non-motile and rod-shaped bacterium, designated strain A5Q-67(T) was isolated from leaf litter collected at the mangrove estuary of Nakama River, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate was affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (94.2 %) to Imtechella halotolerans K1(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain A5Q-67(T) were identified as iso-C17:0 3-OH, summed feature 1 (iso-C15:1 H and/or C13:0 3-OH) and iso-C15:0 as defined by the MIDI system. The DNA G+C content was determined to be 36.7 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Frondibacter aureus gen. nov., sp. nov. is proposed. The type strain of F. aureus is A5Q-67(T) (=KCTC 32991(T) = NBRC 110021(T)). PMID:25385000

  8. A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China

    NASA Astrophysics Data System (ADS)

    Reisz, Robert R.; Liu, Jun; Li, Jin-Ling; Mller, Johannes

    2011-05-01

    Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent.

  9. Cosmosperma polyloba gen. et sp. nov., a seed plant from the Upper Devonian of South China

    NASA Astrophysics Data System (ADS)

    Wang, Deming; Liu, Le; Meng, Meicen; Xue, Jinzhuang; Liu, Tuo; Guo, Yun

    2014-08-01

    Seed plants with ovules were abundant in the Late Devonian of Euramerica and they contribute significantly to our understanding of their early history. However, coeval ovules have been scarce in other regions of the world. Specimens of the seed plant Cosmosperma polyloba gen. et sp. nov. Wang et al. were recently obtained from the Upper Devonian (Famennian) Wutong Formation, at Fanwan Village, Changxing County, Zhejiang Province, China. This new seed plant has cupulate ovules, the uniovulate cupules with up to 16 distal segments and with minute spines on the outer surface, synangiate pollen organs bearing six to eight microsporangia fused only at the base, and planate and highly dissected pinnules in alternate arrangement. It differs from other Devonian seed plants mainly in the organization and position of the uniovulate and ornamented cupule, and in the highly dissected pinnules. Cosmosperma Wang et al. represents the first Devonian ovules recovered from China or eastern Asia and further illustrates the diversity of early spermatophytes. As for the Late Devonian seed plants, it is suggested that the pollen organs are synangiate and simple in organization, and the branches and leaves are generally planate.

  10. Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales.

    PubMed

    Nesb, Camilla L; Bradnan, Danielle M; Adebusuyi, Abigail; Dlutek, Marlena; Petrus, Amanda K; Foght, Julia; Doolittle, W Ford; Noll, Kenneth M

    2012-05-01

    A novel mesophilic member of the Thermotogales, strain MesG1.Ag.4.2, was isolated from sediments from Baltimore Harbor, MD, USA. The strain grew optimally at 37C with a doubling time of 16.5h on xylose. Carbohydrates and proteinaceous compounds supported growth and pentoses were preferred over hexoses. The strain was strictly anaerobic and growth was slightly stimulated by thiosulfate, sulfite, and elemental sulfur. The G+C content of its genomic DNA was 45.3mol%. Strain MesG1.Ag.4.2 and Kosmotoga olearia lipids were analyzed. Strain MesG1.Ag.4.2 contained no long-chain dicarboxylic acids and its major phospholipid was lyso-phosphatidylserine. Long-chain dicarboxylic acids were found in K. olearia and its major phospholipid was cardiolipin, a lipid not yet reported in Thermotogales species. Phylogenetic analyses of its two 16S rRNA genes placed strain MesG1.Ag.4.2 within the bacterial order Thermotogales. Based on the phylogenetic analyses and its low optimal growth temperature, it is proposed that the strain represents a novel species of a new genus within the family Thermotogaceae, order Thermotogales. The name Mesotoga prima gen. nov., sp. nov. is proposed. The type strain of M. prima is MesG1.Ag.4.2 (=DSM 24739=ATCC BAA-2239). PMID:22411358

  11. Sapocribrum chincoteaguense n. gen. n. sp.: A Small, Scale-bearing Amoebozoan with Flabellinid Affinities.

    PubMed

    Lahr, Daniel J G; Grant, Jessica; Molestina, Robert; Katz, Laura A; Anderson, O Roger

    2015-01-01

    The isolate American Type Culture Collection (ATCC) 50979 is a small amoebozoan whose actin gene was previously characterized, but did not allow a stable phylogenetic placement. This isolate was originally mis-identified upon deposition, and subsequently mis-illustrated in a recent publication. Here, we provide both a detailed morphological description as well as additional molecular analyses in order to clarify the isolate's phylogenetic relationships. The amoeba is minute (less than 5 ?m), and presents the behavior of staying in a fixed location, while emitting one or two thin pseudopods. Transmission electron microscopy reveals that the cell is covered in a layer with embedded scales, giving the cell an armored appearance. Molecular phylogenetic analyses of data (actin, alpha- and beta-tubulin, elongation factor 2, and 14-3-3) from transcriptomes of this and four other isolates reveals that ATCC 50979() is closely related to the recently described Squamamoeba japonica and in a novel, stable clade. Due to the unique nature of the scale covering, as well as other gross morphological characters and the molecular phylogenetic analyses, we formally describe the isolate as Sapocribrum chincoteaguense n. gen. n. sp. PMID:25515047

  12. Phylogeny and classification of Cercomonadida (Protozoa, Cercozoa): Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. nov.

    PubMed

    Bass, David; Howe, Alexis T; Mylnikov, Alexandre P; Vickerman, Keith; Chao, Ema E; Edwards Smallbone, James; Snell, Jemma; Cabral, Charles; Cavalier-Smith, Thomas

    2009-11-01

    Cercomonads (=Cercomonadida) are biflagellate gliding bacterivorous protozoa, abundant and diverse in soil and freshwater. We establish 56 new species based on 165 cultures, differential interference contrast microscopy, and 18S and ITS2 rDNA sequencing, and a new genus Cavernomonas studied by scanning electron microscopy. We fundamentally revise the phylogeny and classification of cercomonad Cercozoa. We describe 40 Cercomonas species (35 novel), six Eocercomonas (five novel), two Cavernomonas, and 18 Paracercomonas species (14 novel). We obtained additional cercomonad clade A (Cercomonas, Eocercomonas, Cavernomonas) sequences from multiple environmental DNA libraries. The most commonly cultivated genotypes are not the commonest in environmental DNA, suggesting that cercomonad ecology is far more complex than implied by laboratory cultures. Cercomonads have never been isolated from saline environments, although some species can grow in semi-saline media in the laboratory, and environmental DNA libraries regularly detect them in coastal marine sediments. The first ultrastructural study of an anaerobic cercozoan, Paracercomonas anaerobica sp. nov., a highly divergent cercomonad, shows much simpler ciliary roots than in clade A cercomonads, a ciliary hub-lattice and axosome, and mitochondria with tubular cristae, consistent with it being only facultatively anaerobic. We also describe Agitata tremulans gen. et sp. nov., previously misidentified as Cercobodo (=Dimastigamoeba) agilis Moroff. PMID:19589724

  13. Saccharophagus degradans gen. nov., sp. nov., a versatile marine degrader of complex polysaccharides.

    PubMed

    Ekborg, Nathan A; Gonzalez, Jose M; Howard, Michael B; Taylor, Larry E; Hutcheson, Steven W; Weiner, Ronald M

    2005-07-01

    Gammaproteobacteria belonging and related to the genus Microbulbifer are an emerging group of complex carbohydrate-degrading marine bacteria. Previously, all of the representatives were placed within Microbulbifer or were unclassified. Recently, a new genus, Teredinibacter, represented by a single species, Teredinibacter turnerae, was formed to include an endosymbiotic branch of these organisms. In this study, based on 16S rRNA gene sequence similarity and phenotypic analyses, a new genus, Saccharophagus, is proposed to accommodate the most versatile marine carbohydrate degrader yet identified, Saccharophagus degradans gen. nov., sp. nov. 2-40(T) (=ATCC 43961(T)=DSM 17024(T)). S. degradans strain 2-40(T) can degrade 10 tested complex polysaccharides: agar, alginate, chitin, cellulose, fucoidan, laminarin, pectin, pullulan, starch and xylan. S. degradans 2-40(T) shares 90.5% 16S rRNA gene sequence similarity with the type strain of the Microbulbifer type species, Microbulbifer hydrolyticus IRE-31(T), and 91.5% with T. turnerae T7902(T), and can be further distinguished from members of these two genera by 16S rRNA gene cluster analysis, the ability to utilize 10 different complex polysaccharides as sole carbon sources, a significantly lower G+C content and differences in fatty acid content. The three genera of complex polysaccharide-degrading, marine bacteria now encompass 20 strains from diverse marine niches. PMID:16014479

  14. Haloglycomyces albus gen. nov., sp. nov., a halophilic, filamentous actinomycete of the family Glycomycetaceae.

    PubMed

    Guan, Tong-Wei; Tang, Shu-Kun; Wu, Jin-Yuan; Zhi, Xiao-Yang; Xu, Li-Hua; Zhang, Li-Li; Li, Wen-Jun

    2009-06-01

    A novel halophilic actinobacterium, designated YIM 92370(T), was isolated from a hypersaline habitat in Xinjiang Province, north-west China. The strain was aerobic, Gram-positive-staining and halophilic, with an optimum NaCl concentration for growth of 8-12 % (w/v). The whole-cell sugar pattern consisted of ribose, xylose and glucose. The predominant menaquinone was MK-9(H(4)) and the major fatty acids were iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0). The phospholipid pattern consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phosphoglycolipids and one unknown phospholipid. The G+C content of the genomic DNA was 60.8 mol%. Phylogenetic analysis showed that strain YIM 92370(T) can be distinguished from representatives of Glycomyces and Stackebrandtia, the two existing genera in the family Glycomycetaceae, by low 16S rRNA gene sequence similarities (<93.7 %). Strain YIM 92370(T) therefore represents a novel genus and species of the family Glycomycetaceae, for which the name Haloglycomyces albus gen. nov., sp. nov. is proposed. The type strain of Haloglycomyces albus is YIM 92370(T) (=DSM 45210(T) =KCTC 19481(T)). PMID:19502305

  15. Microvirga subterranea gen. nov., sp. nov., a moderate thermophile from a deep subsurface Australian thermal aquifer.

    PubMed

    Kanso, Sungwan; Patel, Bharat K C

    2003-03-01

    A strictly aerobic bacterium, strain Fail4T, was isolated from free-flowing geothermal waters of a bore (bore register no. 3768) tapping the Great Artesian Basin of Australia. The non-sporulating, Gram-negative cells of strain Fail4T produced light-pink colonies, were rod-shaped (1 x 1.5-4 microm) and were motile by a single polar flagellum. Strain Fail4T grew optimally at 41 degrees C at a pH of 7.0 and had an absolute requirement for yeast extract. The strain grew on casein hydrolysate, tryptone, gelatin, xylose and acetate in a medium supplemented with 0.06 or 0.006% yeast extract. Weak acid production was detected from glucose and arabinose. Catalase was produced. Nitrite was produced from nitrate. Strain Fail4T was sensitive to antibiotics that inhibit growth of bacteria. The G + C content was 63.5 +/- 0.5 mol%. Strain Fail4T was a member of the class 'Alphaproteobacteria', phylum Proteobacteria, placed almost equidistantly between Methylobacterium species, Chelatococcus asaccharovorans and Bosea thiooxidans (similarity value of 93%) as its nearest phylogenetic relatives. Phylogenetic and phenotypic evidence suggest that strain Fail4T (=ATCC BAA-295T = DSM 14364T) should be placed as the type strain of a species in a newly created genus, for which the name Microvirga subterranea gen. nov., sp. nov. is proposed. PMID:12710604

  16. Taonella mepensis gen. nov., sp. nov., a member of the family Rhodospirillaceae isolated from activated sludge.

    PubMed

    Xi, Xue-dong; Dong, Wei-liang; Zhang, Jun; Huang, Yan; Cui, Zhong-li

    2013-07-01

    A novel Gram-negative, non-spore-forming, rod-shaped strain, H1(T), was isolated from activated sludge by micromanipulation. No close relatives among cultured bacterial isolates were found; phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H1(T) forms a deep single branch in the family Rhodospirillaceae. Cells of strain H1(T) were slightly curved to straight rods (1.2-1.4 1.5-1.7 m) and motile by a single polar flagellum. Strain H1(T) was able to grow in the presence of 0-4 % NaCl and grew optimally at 37 C and pH 6.0-7.0. Chemotaxonomic analysis revealed that strain H1(T) possessed Q-10 as the predominant ubiquinone and C18 : 1?7c, C16 : 0 and C19 : 0 cyclo ?8c as the major fatty acids. The DNA G+C content of strain H1(T) was 65.1 mol%. Comparative analysis of 16S rRNA gene sequences, and phenotypic and chemotaxonomic data, indicate that strain H1(T) should represent a novel genus and species of the family Rhodospirillaceae. The name Taonella mepensis gen. nov., sp. nov. is proposed. The type strain of Taonella mepensis is H1(T) ( = CICC 10529(T) = CCTCC AB 2012861(T) = KACC 16940(T)). PMID:23223814

  17. GenEvA (I): a new framework for event generation

    NASA Astrophysics Data System (ADS)

    Bauer, Christian W.; Tackmann, Frank J.; Thaler, Jesse

    2008-12-01

    We show how many contemporary issues in event generation can be recast in terms of partonic calculations with a matching scale. This framework is called GenEvA, and a key ingredient is a new notion of phase space which avoids the problem of phase space double-counting by construction and includes a built-in definition of a matching scale. This matching scale can be used to smoothly merge any partonic calculation with a parton shower. The best partonic calculation for a given region of phase space can be determined through physics considerations alone, independent of the algorithmic details of the merging. As an explicit example, we construct a positive-weight partonic calculation for e+e- ? n jets at next-to-leading order (NLO) with leading-logarithmic (LL) resummation. We improve on the NLO/LL result by adding additional higher-multiplicity tree-level (LO) calculations to obtain a merged NLO/LO/LL result. These results are implemented using a new phase space generator introduced in a companion paper [1].

  18. Flavicella marina gen. nov., sp. nov., a carotenoid-producing bacterium from surface seawater.

    PubMed

    Teramoto, Maki; Nishijima, Miyuki

    2015-03-01

    A Gram-stain-negative, non-motile, mesophilic, aerobic, rod-shaped or spherical bacterium, strain 2A-7(T), was isolated from surface seawater at Muroto city, Kochi prefecture, Japan. The strain produced a pigment(s), the absorption spectrum of which closely resembled that of ?-carotene. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain fell within the family Flavobacteriaceae and clustered distantly with the type strains of species of the genus Lutibacter (up to 93.9?% similarity). The DNA G+C content was 34.1 mol%. The major fatty acids were summed feature 3 (iso-C15?:?0 2-OH and/or C16?:?1?7c), iso-C17?:?0 3-OH and iso-C15?:?0 3-OH. The major polar lipids were phosphatidylethanolamine and three unidentified lipids. Menaquinone 6 was detected as the sole isoprenoid quinone. On the basis of phenotypic, genotypic and chemotaxonomic data, strain 2A-7(T) represents a novel genus and species, for which the name Flavicella marina gen. nov., sp. nov. is proposed. The type strain of Flavicella marina is 2A-7(T) (?=?NBRC 110145(T)?=?KCTC 42197(T)). PMID:25481292

  19. Thermogladius shockii gen. nov., sp. nov., a hyperthermophilic crenarchaeote from Yellowstone National Park, USA.

    PubMed

    Osburn, Magdalena R; Amend, Jan P

    2011-01-01

    A hyperthermophilic heterotrophic archaeon (strain WB1) was isolated from a thermal pool in the Washburn hot spring group of Yellowstone National Park, USA. WB1 is a coccus, 0.6-1.2 ?m in diameter, with a tetragonal S-layer, vacuoles, and occasional stalk-like protrusions. Growth is optimal at 84C (range 64-93C), pH 5-6 (range 3.5-8.5), and <1 g/l NaCl (range 0-4.6 g/l NaCl). Tests of metabolic properties show the isolate to be a strict anaerobe that ferments complex organic substrates. Phylogenetic analysis of the 16S rRNA gene sequence places WB1 in a clade of previously uncultured Desulfurococcaceae and shows it to have ? 96% 16S rRNA sequence identity to Desulfurococcus mobilis, Staphylothermus marinus, Staphylothermus hellenicus, and Sulfophobococcus zilligii. The 16S rRNA gene contains a large insertion similar to homing endonuclease introns reported in Thermoproteus and Pyrobaculum species. Growth is unaffected by the presence of S(0) or SO(4)(2-), thereby differentiating the isolate from its closest relatives. Based on phylogenetic and physiological differences, it is proposed that isolate WB1 represents the type strain of a novel genus and species within the Desulfurococcaceae, Thermogladius shockii gen. nov., sp. nov. (RIKEN = JCM-16579, ATCC = BAA-1607, Genbank 16S rRNA gene = EU183120). PMID:20978744

  20. Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees.

    PubMed

    Kwong, Waldan K; Moran, Nancy A

    2016-03-01

    Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29-31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T). PMID:26743158

  1. Tachornithoglyphus gen. nov.-a new genus of nidicolous Pyroglyphidae(Acariformes: Astigmata).

    PubMed

    Klimov, Pavel B; Bochkov, Andre V; Oconnor, Barry M

    2015-01-01

    Tachornithoglyphus gen. nov. (Acariformes: Pyroglyphidae) is established for Tachornithoglyphus tachornis (Cruz, Cuervo and Dusbabek, 1984), comb. nov. (transferred from Guatemalichus), collected from nests of the Antillean palm swift, Tachornis phoenicobia (Apodiformes: Apodidae) in Cuba. The new genus differs from the other four genera of the subfamily Guatemalichinae, Guatemalichus Fain and Wharton, 1970, Pottocola Fain, 1971, Fainoglyphus Atyeo and Gaud, 1977, and Capitonocoptes Fain and Gaud, 1984, mainly by having the length of solenidion ?1 of genu I less than one-third that of the segment (vs. solenidion ?1I at least half as long as genu I), by the absence of famulus ? on tarsus I (vs. present), and by coxal apodemes Ia separated from each other and contiguous to the lateral parts of the epigynal arch (vs. posterior tips of apodemes Ia fused to each other and with the median part of the epigynal arch, or separated and contiguous to or fused with the median part of the epigynal arch). A detailed redescription of adults and tritonymphs of T. tachornis is provided. PMID:26248906

  2. Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water.

    PubMed

    Poroshina, Maria N; Trotsenko, Yuri A; Doronina, Nina V

    2015-04-01

    An aerobic halotolerant restricted facultatively methylotrophic bacterium was isolated from a saline hot spring in Pamukkale, Turkey, and designated strain PK2(T). The cells of this strain were Gram-stain-negative, asporogenous, motile short rods multiplying by binary fission. They utilized methanol, methylamine and mannitol as carbon and energy sources. The organism grew optimally at 30 C in media containing 85 mM NaCl and at pH 7.5-8.0. C1 compounds were assimilated via the isocitrate-lyase-positive variant of the serine pathway. Poly-?-hydroxybutyrate and the compatible solute ectoine were found in the cells. The dominant phospholipids were phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The major cellular fatty acids of methanol-grown cells were C(18?:?1)?7 and C(16?:?1)?7c. The main ubiquinone was Q-10. The DNA G+C content was 67.9 mol% (T(m)). The 16S rRNA gene sequence suggests that strain PK2(T) is affiliated with the order Rhizobiales within the class Alphaproteobacteria , being most closely related to Mesorhizobium gobiense CCBAU 83330(T) (94% similarity). A novel genus and species, Methylobrevis pamukkalensis gen. nov., sp. nov., is proposed on the basis of phenotypic and genotypic data, with PK2(T) (VKM B-2849(T)?=?JCM 30229(T)) as the type strain. PMID:25667389

  3. Functional Allocation for Ground-Based Automated Separation Assurance in NextGen

    NASA Technical Reports Server (NTRS)

    Prevot, Thomas; Mercer, Joey; Martin, Lynne; Homola, Jeffrey; Cabrall, Christopher; Brasil, Connie

    2010-01-01

    As part of an ongoing research effort into functional allocation in a NextGen environment, a controller-in-the-loop study on ground-based automated separation assurance was conducted at NASA Ames' Airspace Operations Laboratory in February 2010. Participants included six FAA front line managers, who are currently certified professional controllers and four recently retired controllers. Traffic scenarios were 15 and 30 minutes long where controllers interacted with advanced technologies for ground-based separation assurance, weather avoidance, and arrival metering. The automation managed the separation by resolving conflicts automatically and involved controllers only by exception, e.g., when the automated resolution would have been outside preset limits. Results from data analyses show that workload was low despite high levels of traffic, Operational Errors did occur but were closely tied to local complexity, and safety acceptability ratings varied with traffic levels. Positive feedback was elicited for the overall concept with discussion on the proper allocation of functions and trust in automation.

  4. Hypnocyclicus thermotrophus gen. nov., sp. nov. isolated from a microbial mat in a hydrothermal vent field.

    PubMed

    Roalkvam, Irene; Bredy, Florian; Baumberger, Tamara; Pedersen, Rolf-B; Steen, Ida Helene

    2015-12-01

    The bacterial strain, IR-2T, was isolated from a microbial mat sampled near a hydrothermal vent in the Greenland Sea. Phylogenetic analysis, based on the 16S rRNA gene, showed that the?closest relatives of IR-2T were Ilyobacter tartaricus, Ilyobacter insuetus, Propionigenium modestum and Fusobacterium varium (91?% 16S rRNA gene sequence similarity). The cells of?the novel strain were Gram-stain-negative and pleomorphic; changing from long motile rods to non-motile ring structures during the growth cycle. Growth occurred at 20-55?C (optimally at 48?C), with 1-6?% (w/v) NaCl (optimally with 2?%), and at pH?5.3-8.0 (optimally at pH?6.0-8.0). The strain had obligate fermentative growth on various sugars and yeast extract. The DNA G+C content of strain IR-2T was 25.7?mol%. The cell sugars comprised mainly ribose, mannose and glucose, while the main polar lipids were glycolipids, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. The fatty acid content of strain IR-2 was?dominated by saturated and unsaturated iso-branched or anteiso-branched forms. Strain IR-2 represents a novel genus and species, for which the name Hypnocyclicus thermotrophus gen. nov., sp. nov. is proposed. The type strain is IR-2T (?=?DSM 100055?=?JCM 30901). PMID:26373292

  5. GenInfoGuardA Robust and Distortion-Free Watermarking Technique for Genetic Data

    PubMed Central

    Khan, Sharifullah; Anwar, Zahid; Kamran, Muhammad

    2015-01-01

    Genetic data, in digital format, is used in different biological phenomena such as DNA translation, mRNA transcription and protein synthesis. The accuracy of these biological phenomena depend on genetic codes and all subsequent processes. To computerize the biological procedures, different domain experts are provided with the authorized access of the genetic codes; as a consequence, the ownership protection of such data is inevitable. For this purpose, watermarks serve as the proof of ownership of data. While protecting data, embedded hidden messages (watermarks) influence the genetic data; therefore, the accurate execution of the relevant processes and the overall result becomes questionable. Most of the DNA based watermarking techniques modify the genetic data and are therefore vulnerable to information loss. Distortion-free techniques make sure that no modifications occur during watermarking; however, they are fragile to malicious attacks and therefore cannot be used for ownership protection (particularly, in presence of a threat model). Therefore, there is a need for a technique that must be robust and should also prevent unwanted modifications. In this spirit, a watermarking technique with aforementioned characteristics has been proposed in this paper. The proposed technique makes sure that: (i) the ownership rights are protected by means of a robust watermark; and (ii) the integrity of genetic data is preserved. The proposed techniqueGenInfoGuardensures its robustness through the watermark encoding in permuted values, and exhibits high decoding accuracy against various malicious attacks. PMID:25689741

  6. Decay Heat Removal in GEN IV Gas-Cooled Fast Reactors

    DOE PAGESBeta

    Cheng, Lap-Yan; Wei, Thomas Y. C.

    2009-01-01

    The safety goal of the current designs of advanced high-temperature thermal gas-cooled reactors (HTRs) is that no core meltdown would occur in a depressurization event with a combination of concurrent safety system failures. This study focused on the analysis of passive decay heat removal (DHR) in a GEN IV direct-cycle gas-cooled fast reactor (GFR) which is based on the technology developments of the HTRs. Given the different criteria and design characteristics of the GFR, an approach different from that taken for the HTRs for passive DHR would have to be explored. Different design options based on maintaining core flow weremore » evaluated by performing transient analysis of a depressurization accident using the system code RELAP5-3D. The study also reviewed the conceptual design of autonomous systems for shutdown decay heat removal and recommends that future work in this area should be focused on the potential for Brayton cycle DHRs.« less

  7. Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity.

    PubMed

    Vartoukian, Sonia R; Downes, Julia; Palmer, Richard M; Wade, William G

    2013-02-01

    SGP1(T), a strain belonging to a lineage of the phylum Synergistetes with no previously cultivated representatives was subjected to a comprehensive range of phenotypic and genotypic tests. For good growth the strain was dependent on co-culture with, or extracts from, selected other oral bacteria. Cells of strain SGP1(T) were asaccharolytic and major amounts of acetic acid and moderate amounts of propionic acid were produced as end products of metabolism in peptone-yeast extract-glucose broth supplemented with a filtered cell sonicate of Fusobacterium nucleatum subsp. nucleatum ATCC 25586(T) (25?%, v/v). Hydrogen sulphide was produced and gelatin was weakly hydrolysed. The major cellular fatty acids were C(14?:?0), C(18?:?0) and C(16?:?0). The DNA G+C content of strain SGP1(T) was 63 mol%. Phylogenetic analysis of the full-length 16S rRNA gene showed that strain SGP1(T) represented a novel group within the phylum Synergistetes. A novel species in a new genus, Fretibacterium fastidiosum gen. nov., sp. nov., is proposed. The type strain of Fretibacterium fastidiosum is SGP1(T) (?=?DSM 25557(T)?=?JCM 16858(T)). PMID:22493171

  8. Comparison of Gen-Probe Group A streptococcus Direct Test with culture for diagnosing streptococcal pharyngitis.

    PubMed

    Pokorski, S J; Vetter, E A; Wollan, P C; Cockerill, F R

    1994-06-01

    The Group A Streptococcus Direct Test (GP-ST test; Gen-Probe, Inc., San Diego, Calif.) was compared with culture for the detection of Streptococcus pyogenes from throat swabs of 767 patients with pharyngitis. Swabs were tested by the GP-ST test after inoculating a 5% sheep blood agar (SBA) plate. SBA plates were incubated at 35 degrees C in room air for 72 h. SBA plates with no evidence of beta-hemolytic colonies after 18 to 24 h of incubation were subcultured by taking a swipe across the primary inoculum from the SBA plate to an agar selective for Streptococcus spp. In a low-prevalence (11.9%) population and in comparison with the number of positive cultures detected by the 72-h single-culture method (SBA plate method), the GP-ST test had a sensitivity of 88.6%, a specificity of 97.8%, a positive predictive value of 83.9%, and a negative predictive value of 98.5%. In comparison with the growth of any colonies of S. pyogenes on the 72-h SBA plates plus a subculture onto selective blood agar, the sensitivities and specificities were as follows: 72-h SBA plate method, 96.7 and 100%, respectively; GP-ST test, 85.7 and 97.8%, respectively. The GP-ST test is an easy-to-perform, reliable test for batch screening of throat swabs for S. pyogenes. PMID:8077386

  9. A new tardigrade, Mutaparadoxipus duodigifinis gen. nov., sp. nov. (Heterotardigrada: Arthrotardigrada), from the Southeastern United States.

    PubMed

    Gross, Vladimir; Miller, William R; Hochberg, Rick

    2014-01-01

    A new genus and species of Arthrotardigrada is described from Florida, USA based on its unique adhesive pad/claw combinations. Mutaparadoxipus duodigifinis gen. nov., sp. nov., is characterized by well-developed, ventral secondary clavae that are adjacent to the mouth, pointed lateral and caudal alae, seminal receptacles with coiled ducts opening lateral to the gonopore, and all legs with digits bearing proximal adhesive pads. Distal claws are present on digits I-III of legs I-III, but are missing from digit IV. On leg IV, distal claws are present only on digits II & III. A single accessory point is present on claws II & III only. This is the fourth species discovered to date with proximal adhesive pads, increasing support for a clade of adhesive-padded arthrotardigrades, and is likely the sister taxon of Paradoxipus orzeliscoides. The incomplete set of claws may represent an evolutionary step in a progressive loss of claws hypothesized to have occurred within the Halechiniscidae. The subfamily Orzeliscinae is amended as a result. PMID:25081448

  10. Taeseokella kangwonensis gen. nov., sp. nov., isolated from a freshwater reservoir.

    PubMed

    Joung, Yochan; Hong, Sunhee; Kim, Haneul; Kang, Heeyoung; Farrance, Christine E; Joh, Kiseong

    2015-12-01

    A Gram-stain-negative, non-motile and yellow-pigmented bacterium, designated HME8275T, was isolated from freshwater in Korea. The major fatty acids of strain HME8275T were summed feature 3 (comprising C16?:?1?6c and/or C16?:?1?7c), C16?:?0 and iso-C15?:?0. The only respiratory quinone was MK-7. Polar lipid analysis showed phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content of strain HME8275T was 37.6?mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8275T formed a lineage within the family Cytophagaceae and was related to Lacihabitans soyangensis HME6675T (92.6?% 16S rRNA gene sequence similarity), Leadbetterella byssophila 4M15T (89.0?%), Fluviimonas pallidilutea TQQ6T (89.7?%) and Emticicia oligotrophica GPTSA100-15T (89.8?%). On the basis of the evidence presented in this study, strain HME8275T represents a novel species of a new genus in the family Cytophagaceae, for which the name Taeseokella kangwonensis, gen. nov., sp. nov. is proposed. The type strain of the type species is HME8275T (?=?KACC 16933T?=?CECT 8198T). PMID:26341781

  11. Future projections of extreme precipitation using Advanced Weather Generator (AWE-GEN) over Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Syafrina, A. H.; Zalina, M. D.; Juneng, L.

    2014-09-01

    A stochastic downscaling methodology known as the Advanced Weather Generator, AWE-GEN, has been tested at four stations in Peninsular Malaysia using observations available from 1975 to 2005. The methodology involves a stochastic downscaling procedure based on a Bayesian approach. Climate statistics from a multi-model ensemble of General Circulation Model (GCM) outputs were calculated and factors of change were derived to produce the probability distribution functions (PDF). New parameters were obtained to project future climate time series. A multi-model ensemble was used in this study. The projections of extreme precipitation were based on the RCP 6.0 scenario (2081-2100). The model was able to simulate both hourly and 24-h extreme precipitation, as well as wet spell durations quite well for almost all regions. However, the performance of GCM models varies significantly in all regions showing high variability of monthly precipitation for both observed and future periods. The extreme precipitation for both hourly and 24-h seems to increase in future, while extreme of wet spells remain unchanged, up to the return periods of 10-40 years.

  12. Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples.

    PubMed

    Humrighouse, B W; Emery, B D; Kelly, A J; Metcalfe, M G; Mbizo, J; McQuiston, J R

    2016-04-01

    A Gram-negative, aerobic, motile, spiral-shaped bacterium, strain H5569(T), was isolated from a human blood sample. Phenotypic and molecular characteristics of the isolate were investigated. Optimal growth was found to occur at 35 °C under aerobic conditions on Heart Infusion Agar supplemented with 5 % rabbit blood. The major fatty acids present in the cells were identified as C16:0, C16:1ω7c and C18:1ω7c. The predominant respiratory quinone was found to be ubiquinone-Q10. The G+C content of genomic DNA for strain H5569(T) was found to be 49.9 %. Based on 16S rRNA gene sequence analysis results, 13 additional isolates were also analysed in this study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism, represented by strain H5569(T), forms a distinct lineage within the family Rhodospirillaceae, closely related to two Novispirillum itersonii subspecies (93.9-94.1 %) and two Caenispirillum sp. (91.2-91.6 %). Based on these results, the isolate H5569(T) is concluded to represent a new genus and species for which the name Haematospirillum jordaniae gen. nov., sp. nov. is proposed. The type strain is H5569(T) (=DSM(T) 28903 = CCUG 66838(T)). PMID:26857139

  13. A new captorhinid reptile, Gansurhinus qingtoushanensis, gen. et sp. nov., from the Permian of China.

    PubMed

    Reisz, Robert R; Liu, Jun; Li, Jin-Ling; Mller, Johannes

    2011-05-01

    Captorhinids, a clade of Paleozoic reptiles, are represented by a rich fossil record that extends from the Late Carboniferous into the Late Permian. Representatives of this clade dispersed from the equatorial regions of Laurasia into the temperate regions of Pangea during the Middle and Late Permian. This rich fossil record shows that there was an evolutionary trend from faunivorous to omnivorous and herbivorous feeding habits within this clade. The discovery of well-preserved captorhinid materials in the Middle Permian of China allows us to determine that the new taxon, Gansurhinus qingtoushanensis, gen. et sp. nov, is a member of Moradisaurinae, a clade of captorhinids with multiple tooth rows arranged in parallel. The presence of this moradisaurine in the Middle Permian of south central Asia leads us to suggest that paleogeographic changes during the Permian, with part of what is today China becoming a large peninsula of Pangea, allowed these early reptiles as well as other terrestrial vertebrates to extend their geographic ranges to this region of the Late Paleozoic supercontinent. PMID:21484260

  14. Kabataia gen. n., a new genus proposed for Microsporidium spp. infecting trunk muscles of fishes.

    PubMed

    Lom, J; Dykov, I; Tonguthai, K

    1999-10-11

    Based on a fine structural study, a new genus, Kabataia gen. n., is proposed for Microsporidium arthuri Lom, Dykov and Shaharom, 1990. It develops in trunk muscles of a South-East Asian freshwater fish, Pangasius sutchi. The genus has nuclei isolated throughout the cycle, merogony stages are multinucleate, sporogony proceeds in 2 steps: multinucleate sporont segments into sporoblast mother cells which produce 2 sporoblasts. Sporoblasts and early spores are characterized by a dense globule at the site of the posterior vacuole. Mature spores are of a rather variable shape. Their exospore is raised into small, irregular fields. The polaroplast is relatively small and its posterior part consists of flat vesicles with dense contents. The polar tube makes a small number (4 to 6) of turns. A congeneric species is Kabataia seriolae (Egusa, 1982) comb. nov. from cultured marine yellowtails Seriola quinqueradiata. Kabataia inflicts heavy damage on muscle tissue. The sarcoplasm within which Kabataia develops is reduced to an amorphous mass with tubule-like fibrils, microfibrils and small vesicles. PMID:10590927

  15. Methods for Estimating Environmental Effects and Constraints on NexGen: High Density Case Study

    NASA Technical Reports Server (NTRS)

    Augustine, S.; Ermatinger, C.; Graham, M.; Thompson, T.

    2010-01-01

    This document provides a summary of the current methods developed by Metron Aviation for the estimate of environmental effects and constraints on the Next Generation Air Transportation System (NextGen). This body of work incorporates many of the key elements necessary to achieve such an estimate. Each section contains the background and motivation for the technical elements of the work, a description of the methods used, and possible next steps. The current methods described in this document were selected in an attempt to provide a good balance between accuracy and fairly rapid turn around times to best advance Joint Planning and Development Office (JPDO) System Modeling and Analysis Division (SMAD) objectives while also supporting the needs of the JPDO Environmental Working Group (EWG). In particular this document describes methods applied to support the High Density (HD) Case Study performed during the spring of 2008. A reference day (in 2006) is modeled to describe current system capabilities while the future demand is applied to multiple alternatives to analyze system performance. The major variables in the alternatives are operational/procedural capabilities for airport, terminal, and en route airspace along with projected improvements to airframe, engine and navigational equipment.

  16. Emergency Decay Heat Removal in a GEN-IV Gas-Cooled Fast Reactor

    SciTech Connect

    Cheng, Lap Y.; Ludewig, Hans; Jo, Jae

    2006-07-01

    A series of transient analyses using the system code RELAP5-3d has been performed to confirm the efficacy of a proposed hybrid active/passive combination approach to the decay heat removal for an advanced 2400 MWt GEN-IV gas-cooled fast reactor. The accident sequence of interest is a station blackout simultaneous with a small break (10 sq.inch/0.645 m{sup 2}) in the reactor vessel. The analyses cover the three phases of decay heat removal in a depressurization accident: (1) forced flow cooling by the power conversion unit (PCU) coast down, (2) active forced flow cooling by a battery powered blower, and (3) passive cooling by natural circulation. The blower is part of an emergency cooling system (ECS) that by design is to sustain passive decay heat removal via natural circulation cooling 24 hours after shutdown. The RELAP5 model includes the helium-cooled reactor, the ECS (primary and secondary side), the PCU with all the rotating machinery (turbine and compressors) and the heat transfer components (recuperator, pre-cooler and inter-cooler), and the guard containment that surrounds the reactor and the PCU. The transient analysis has demonstrated the effectiveness of passive decay heat removal by natural circulation cooling when the guard containment pressure is maintained at or above 800 kPa. (authors)

  17. Spelaeicoccus albus gen. nov., sp. nov., an actinobacterium isolated from a natural cave.

    PubMed

    Lee, Soon Dong

    2013-11-01

    A novel Gram-stain-positive, non-endospore-forming, coccoid actinobacterium, designated strain D3-40(T), was isolated from the soil of a natural cave and characterized by means of a polyphasic taxonomic analysis. 16S rRNA gene sequence analysis showed that strain D3-40(T) is a member of the suborder Micrococcineae and forms a distinct branch at the base of a Brevibacteriaceae cluster. Its closest relative is the type strain of Brevibacterium samyangense (95.7?% sequence similarity). The chemotaxonomic characteristics were as follows: the cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid; the major menaquinone was MK-9(H2); the polar lipids consisted of phosphatidylglycerol, phosphatidylinositol, an unknown glycolipid and an unknown phospholipid; the major fatty acids were anteiso-C15?:?0, anteiso-C17?:?0, iso-C15?:?0, C16?:?0 and cyclohexyl-C17?:?0; mycolic acids were absent. The G+C content of the DNA was 64.3 mol%. On the basis of morphological, chemotaxonomic and phylogenetic data, it is suggested that the organism represents a novel species of a new genus within the family Brevibacteriaceae, for which the name Spelaeicoccus albus gen. nov., sp. nov. is proposed. The type strain of the type species is D3-40(T) (?=?KCTC 29141(T)?=?DSM 26341(T)). PMID:23811133

  18. Aquihabitans daechungensis gen. nov., sp. nov., an actinobacterium isolated from reservoir water.

    PubMed

    Jin, Long; Huy, Hangsak; Kim, Kwang Kyu; Lee, Hyung-Gwan; Kim, Hee-Sik; Ahn, Chi-Yong; Oh, Hee-Mock

    2013-08-01

    A novel Gram-reaction-positive bacterium, strain CH22-21(T), was isolated from a water sample taken from Daechung Reservoir, Republic of Korea, during the late-blooming period of cyanobacteria. Cells of strain CH22-21(T) were non-motile, ciliated short rods that formed creamy-white colonies on half-strength modified R2A agar. Chemotaxonomic results showed menaquinone MK-9(H6) as the predominant respiratory menaquinone, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside as major polar lipids, 16 : 1?5c, 16 : 0, 17 : 1?8c and 18 : 1?9c as major fatty acids, and a DNA G+C content of 71.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the strain formed a separate lineage within the order Acidimicrobiales, showing similarity values of <92.3 % with its closest phylogenetic neighbours. The combined genotypic and phenotypic data showed that strain CH22-21(T) could be distinguished from all genera within the order Acidimicrobiales and represented a novel species of a new genus in the family Iamiaceae, for which the name Aquihabitans dachungensis gen. nov., sp. nov. is proposed. The type strain of Aquihabitans dachungensis is CH22-21(T) (= KCTC 19849(T) = JCM 17787(T)). PMID:23378111

  19. Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium.

    PubMed

    van Gelder, Antonie H; Sousa, Diana Z; Rijpstra, W Irene C; Damst, Jaap S Sinninghe; Stams, Alfons J M; Snchez-Andrea, Irene

    2014-07-01

    A novel anaerobic succinate-producing bacterium, strain ZWB(T), was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4-0.5 m in diameter and 2-3 m in length), and stained Gram-negative. The temperature range for growth was 25-40 C, with an optimum at 37 C. The pH range for growth was 7.0-9.0, with an optimum at pH 7.5. Strain ZWB(T) was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWB(T). The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14 : 0 and iso-C16?:?0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWB(T) belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006(T) (92.1%). Based on the physiological features and phylogenetic analysis, strain ZWB(T) represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWB(T) (?= DSM 27333(T)?= JCM 19283(T)). PMID:24776531

  20. Paraoerskovia marina gen. nov., sp. nov., an actinobacterium isolated from marine sediment.

    PubMed

    Khan, Shams Tabrez; Harayama, Shigeaki; Tamura, Tomohiko; Ando, Katsuhiko; Takagi, Motoki; Kazuo, Shin-ya

    2009-08-01

    A Gram-positive-staining, facultatively anaerobic bacterial strain, CTT-37T, was isolated from a marine sediment sample collected from Tottori city, located on the shore of the Sea of Japan. A 16S rRNA gene sequence comparison indicated that the isolate represents a novel clade that clusters with members of the families Cellulomonadaceae and Sanguibacteraceae. Strain CTT-37T shared maximum 16S rRNA gene sequence similarity of 96.4% with Oerskovia paurometabola DSM 14281T and 96.2% with Oerskovia enterophila DSM 43852T. The DNA-DNA hybridization value between strain CTT-37T and O. enterophila JCM 7350T was 10-12%. The following chemotaxonomic characteristics of strain CTT-37T were markedly different from those of strains in the genus Oerskovia. The cell wall contained L-serine in the peptidoglycan interpeptide bridge. The predominant menaquinone was MK-9 (H4); other quinones detected were MK-9 and MK-9(H2). The only polar lipid was phosphatidylglycerol and the G+C content of the DNA was 70 mol%. Differences in phenotypic characteristics and large phylogenetic distances between strain CTT-37T and all members of the genus Oerskovia supported the classification of CTT-37T within a new genus and species, for which the name Paraoerskovia marina gen. nov., sp. nov. is proposed. The type strain of Paraoerskovia marina is CTT-37T (=NBRC 104352T=DSM 21750T). PMID:19605707

  1. Caenibacterium thermophilum gen. nov., sp. nov., isolated from a thermophilic aerobic digester of municipal sludge.

    PubMed

    Manaia, Clia M; Nunes, Olga C; Nogales, Balbina

    2003-09-01

    A bacterial strain, N2-680(T) (=DSM 15264(T)=LMG 21760(T)), isolated from a thermophilic aerobic digester of municipal sludge, was characterized with respect to its morphology, physiology and taxonomy. Phenotypically, the isolate was a Gram-negative rod with a polar flagellum, catalase- and oxidase-positive, containing cytoplasmic inclusions of poly-beta-hydroxybutyrate and had an optimal growth temperature of about 47 degrees C. Strain N2-680(T) was unable to reduce nitrate and could use organic acids, amino acids and carbohydrates as single carbon sources. Chemotaxonomic analysis revealed that ubiquinone 8 was the major respiratory quinone of this organism and that phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids. At 50 degrees C, the major components in fatty acid methyl ester analysis were C(16 : 0) and cyclo-C(17 : 0). The highest 16S rDNA sequence identity of isolate N2-680(T) was to Leptothrix mobilis and Ideonella dechloratans (95.7 %) and to Rubrivivax gelatinosus and Aquabacterium commune (95.6 %). 16S rDNA sequence similarities to species of two related thermophilic genera, Caldimonas manganoxidans and Tepidimonas ignava, were lower (93.6 and 94.7 %). On the basis of phylogenetic analyses and physiological and chemotaxonomic characteristics, it is proposed that isolate N2-680(T) represents a new genus and species, for which the name Caenibacterium thermophilum gen. nov., sp. nov. is proposed. PMID:13130021

  2. Inhella inkyongensis gen. nov., sp. nov., a new freshwater bacterium in the order Burkholderiales.

    PubMed

    Song, Jaeho; Oh, Hyun-Myung; Lee, Jung-Sook; Woo, Seung-Buhm; Cho, Jang-Cheon

    2009-01-01

    A freshwater bacterium, designated IMCC1713(T), was isolated from a highly eutrophic artificial pond. Cells of the strain were Gram-negative, chemoheterotrophic, polybeat and obligately aerobic short rods that were motile with a single polar flagellum. The 16S rRNA gene sequence similarity analysis showed that the novel strain was most closely related to the species Roseateles depolymerans (96.3%), Mitsuaria chitosanitabida (96.2%), Ideonella dechloratans (96.2%), and Pelomonas saccharophila (96.1%) in the Sphaerotilus-Leptothrix group within the order Burkholderiales. Phylogenetic trees based on 16S rRNA gene sequences indicated that the isolate formed an independent monophyletic clade within the order Burkholderiales. The relatively low DNA G+C content (57.4 mol%), together with several phenotypic characteristics, differentiated the novel strain from other members of the Sphaerotilus-Leptothrix group. From the taxonomic data, therefore, the strain should be classified as a novel genus and species, for which the name Inhella inkyongensis gen. nov., sp. nov. is proposed. The type strain of the proposed species is strain IMCC1713(T) (=KCTC 12791(T)=NBRC 103252(T)=CCUG 54308(T)). PMID:19190402

  3. Caldimonas manganoxidans gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading, manganese-oxidizing thermophile.

    PubMed

    Takeda, Minoru; Kamagata, Yoichi; Ghiorse, William C; Hanada, Satoshi; Koizumi, Jun-ichi

    2002-05-01

    A poly(3-hydroxybutyrate) (PHB)-degrading, gram-negative, aerobic bacterium, strain HS(T), was isolated from a hot spring and chemotaxonomically and phylogenetically characterized. The oxidase-positive, weakly catalase-positive, non-pigmented cells (0.6 x 2.6 microm) exhibited a single polar flagellum and accumulated PHB granules. Strain HS(T) was capable of manganese oxidation. Highest growth rate was attained at 50 degrees C. The optimum pH for growth was 7-8. The major respiratory quinone was ubiquinone-8 and major cellular fatty acids were C16:0, C16:1 and C18:1. The G+C content of the DNA was 66.2 mol%. Comparative 16S rDNA analysis indicated that strain HS(T) is related to the Rubrivivax subgroup and the family Comamonadaceae. The nearest phylogenetic relatives were Ideonella dechloratans (92.1% similarity), Leptothrix discophora (93.6%), Roseateles depolymerans (92.4%) and Rubrivivax gelatinosus (92.2%). On the basis of its phylogenetic and phenotypic properties, it is proposed that this isolate be designated Caldimonas manganoxidans gen. nov., sp. nov.; the type strain is HS(T) (= JCM 10698T = IFO 16448T = ATCC BAA-369T). PMID:12054255

  4. Synthetic and Enhanced Vision Systems for NextGen (SEVS) Simulation and Flight Test Performance Evaluation

    NASA Technical Reports Server (NTRS)

    Shelton, Kevin J.; Kramer, Lynda J.; Ellis,Kyle K.; Rehfeld, Sherri A.

    2012-01-01

    The Synthetic and Enhanced Vision Systems for NextGen (SEVS) simulation and flight tests are jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA). The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SEVS operational and system-level performance capabilities. Nine test flights (38 flight hours) were conducted over the summer and fall of 2011. The evaluations were flown in Gulfstream.s G450 flight test aircraft outfitted with the SEVS technology under very low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 ft to 2400 ft visibility) into various airports from Louisiana to Maine. In-situ flight performance and subjective workload and acceptability data were collected in collaboration with ground simulation studies at LaRC.s Research Flight Deck simulator.

  5. Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota.

    PubMed

    Liu, Min-Jiao; Zhu, Wen-Yong; Li, Jie; Zhao, Guo-Zhen; Xiong, Zhi; Park, Dong-Jin; Hozzein, Wael N; Kim, Chang-Jin; Li, Wen-Jun

    2015-08-01

    An actinomycete strain, designated YIM 690008T, was isolated from Daucus carota collected from South Korea and its taxonomic position was investigated by using a polyphasic approach. The strain grew well on most media tested and no diffusible pigment was produced. The aerial mycelium formed wrinkled single spores and short spore chains, some of which were branched. The whole-cell hydrolysates contained meso-diaminopimelic acid, glucose, mannose, ribose, galactose and rhamnose. The predominant menaquinones were MK-10(H4), MK-10(H6), MK-10(H8) and MK-10(H2). The polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylinositol mannosides, some unknown phospholipids, glycolipids and polar lipids. The major fatty acids were i-C16 : 0, ai-C17 : 0 and C18 : 1ω9c. The DNA G+C content of the genomic DNA was 63.1 mol%. Phylogenetic analysis indicated that the isolate belongs to the family Nocardiopsaceae. However, based on phenotypic, chemotaxonomic and genotypic data, it was concluded that strain YIM 690008T represents a novel genus and novel species of the family Nocardiopsaceae, for which the name Actinorugispora endophytica gen. nov., sp. nov. (type strain YIM 690008T = DSM 46770T = JCM 30099T = KCTC 29480T) is proposed. PMID:25948617

  6. Herminiimonas fonticola gen. nov., sp. nov., a Betaproteobacterium isolated from a source of bottled mineral water.

    PubMed

    Fernandes, Chantal; Rainey, Fred A; Nobre, M Fernanda; Pinhal, Isabel; Folhas, Ftima; da Costa, Milton S

    2005-09-01

    Several yellowish-pigmented bacteria with an optimum growth temperature of about 30 degrees C, were recovered from the source (borehole) of bottled mineral water in the Serra da Estrela in Eastern Portugal. Phylogenetic analyses of the 16S rRNA gene sequence of strains S-94T , S-97, S-99 and S-92 indicated that these organisms represent a new species of the Betaproteobacteria that is not closely related to any other known species. The major fatty acids of the strains are 16:1 omega7c and 16:0. Ubiquinone 8 is the major respiratory quinone. The new isolates are strictly organotrophic and aerobic. The new strains only assimilated organic acids, glycine and alanine. Casamino acids and a mixture of all natural amino acids are not used as sole carbon and nitrogen sources; these are used as nitrogen source in the presence of organic acids. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we are of the opinion that strains S-94T, S-97, S-99 and S-92 represent a new species of a novel genus for which we propose the name Herminiimonas fonticola gen. nov., sp. nov. PMID:16156117

  7. Violaceomyces palustris gen. et sp. nov. and a new monotypic lineage, Violaceomycetales ord. nov. in Ustilaginomycetes.

    PubMed

    Albu, Sebastian; Toome, Merje; Aime, M Catherine

    2015-01-01

    Numerous strains of a novel yeast were isolated in Louisiana, USA, from the leaves of several palustrine plants, most frequently from the invasive aquatic ferns Salvinia minima and S. molesta. This fungus produced fast-growing colonies that were grayish violet to dark blue in culture and rapidly reproduced via production of copious ballistoconidia that germinated to form pseudohyphae. Colonies produced many two-celled yeasts that were distinctly hourglass-or peanut-shaped, and occurred singly or in chains. Phylogenetic analyses of translation elongation factor 1-α, β-tubulin and the nuc rDNA regions encompassing 28S D1-D2 domains, 18S and the internal transcribed spacers 1 and 2, including 5.8S, indicate this fungus is a member of Ustilaginomycetes but holds an isolated position, distinct from the two currently recognized orders, Ustilaginales and Urocystales. Here we describe Violaceomycetales ord. nov., Violaceomycetaceae fam. nov. and Violaceomyces palustris gen. et sp. nov. for this unusual fungus. PMID:26297779

  8. Maeridae from the Indo-Pacific: Elasmopus, Leeuwinella gen. nov., Maeropsis, Pseudelasmopus and Quadrimaera (Amphipoda: Crustacea).

    PubMed

    Hughes, Lauren E

    2015-01-01

    Twenty-two species of Maeridae including the new genus, Leeuwinella, and eight new species are described from Indo-Pacific waters. Leeuwinella mistakensis gen. et sp. nov. from southern Western Australia has dorsal carinae and serrate epimeral margins on pleonites 1-3 and mandibular palp article 3 concave; this significant combination of characters justifies erection of a new genus. Elasmopus coxacallus sp. nov., with a castelloserrate posterior margin of pereopod 7 presents a novel character for the genus, which contains over 100 described species. Elasmopus incomptus sp. nov. and E. norfolkensis sp. nov. are also described from Norfolk Island, South Pacific, while new distribution records are provided for E. gracilis Schellenberg, 1938, E. integer Myers, 1989, and E. molokai J.L. Barnard, 1970 from northwestern Australia, and E. souillacensis Appadoo & Myers, 2003, from the Kermadec Islands. New distribution records for Maeropsis griffini (Berents, 1983) from Bedout Island in Western Australia are the first of the species outside the Queensland type locality and new records of M. thetis (Lowry & Springthorpe, 2005) from mainland Australia to Tasmania and across the Tasman Sea extending its range. Pseudelasmopus walkerae sp. nov. is described from Norfolk Island, and is the second species recorded in the genus, previously known only from Mauritius. Lastly, three new Quadrimaera species, Q. gregoryi, Q. brownorum and Q. vallaris, along with eight known Quadrimaera species, are reported from various locations extending their distributions in the Indo-Pacific. PMID:26701562

  9. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide

    USGS Publications Warehouse

    Schaefer, J.K.; Goodwin, K.D.; McDonald, I.R.; Murrell, J.C.; Oremland, R.S.

    2002-01-01

    A marine methylotroph, designated strain MB2T, was isolated for its ability to grow on methyl bromide as a sole carbon and energy source. Methyl chloride and methyl iodide also supported growth, as did methionine and glycine betaine. A limited amount of growth was observed with dimethyl sulfide. Growth was also noted with unidentified components of the complex media marine broth 2216, yeast extract and Casamino acids. No growth was observed on methylated amines, methanol, formate, acetate, glucose or a variety of other substrates. Growth on methyl bromide and methyl iodide resulted in their oxidation to CO2 with stoichiometric release of bromide and iodide, respectively. Strain MB2T exhibited growth optima at NaCl and Mg2+ concentrations similar to that of seawater. Phylogenetic analysis of the 16S rDNA sequence placed this strain in the ??-Proteobacteria in proximity to the genera Ruegeria and Roseobacter. It is proposed that strain MB2T (= ATCC BAA-92T = DSM 14336T) be designated Leisingera methylohalidivorans gen. nov., sp. nov.

  10. Cosmosperma polyloba gen. et sp. nov., a seed plant from the Upper Devonian of South China.

    PubMed

    Wang, Deming; Liu, Le; Meng, Meicen; Xue, Jinzhuang; Liu, Tuo; Guo, Yun

    2014-08-01

    Seed plants with ovules were abundant in the Late Devonian of Euramerica and they contribute significantly to our understanding of their early history. However, coeval ovules have been scarce in other regions of the world. Specimens of the seed plant Cosmosperma polyloba gen. et sp. nov. Wang et al. were recently obtained from the Upper Devonian (Famennian) Wutong Formation, at Fanwan Village, Changxing County, Zhejiang Province, China. This new seed plant has cupulate ovules, the uniovulate cupules with up to 16 distal segments and with minute spines on the outer surface, synangiate pollen organs bearing six to eight microsporangia fused only at the base, and planate and highly dissected pinnules in alternate arrangement. It differs from other Devonian seed plants mainly in the organization and position of the uniovulate and ornamented cupule, and in the highly dissected pinnules. Cosmosperma Wang et al. represents the first Devonian ovules recovered from China or eastern Asia and further illustrates the diversity of early spermatophytes. As for the Late Devonian seed plants, it is suggested that the pollen organs are synangiate and simple in organization, and the branches and leaves are generally planate. PMID:24965709

  11. Mageeibacillus indolicus gen. nov., sp. nov.: a novel bacterium isolated from the female genital tract.

    PubMed

    Austin, Michele N; Rabe, Lorna K; Srinivasan, Sujatha; Fredricks, David N; Wiesenfeld, Harold C; Hillier, Sharon L

    2015-04-01

    Three isolates of a bacterium recovered from human endometrium using conventional culture methods were characterized biochemically and subjected to 16S rRNA gene sequencing and phylogenetic analysis. Isolates were non-motile, obligately anaerobic, non-spore forming, asaccharolytic, non-cellulolytic, indole positive, Gram positive rods. Cell wall fatty acid profiling revealed C14:0, C16:0, C18:2 ?6, 9c, C18:1 ?9c and C18:0 to be the major fatty acid composition. The DNA mol % G+C was determined to be 44.2%. 16S rRNA gene sequence analysis revealed only 91% sequence similarity with the closest cultivated bacterial isolate, Saccharofermentans acetigenes. Based on genotypic and phenotypic data, all three isolates are considered to be members of the same species and data suggest it represents a novel genus and species in the order Clostridiales with an association with Clostridium rRNA cluster III within the family Ruminococcaceae. We propose the name, Mageeibacillus indolicus gen. nov., sp. nov. The type strain is BAA-2120(T) and CCUG 59143(T). PMID:25482717

  12. New data on two remarkable Antarctic species Amblydorylaimus isokaryon (Loof, 1975) Andrssy, 1998 and Pararhyssocolpus paradoxus (Loof, 1975), gen. n., comb. n. (Nematoda, Dorylaimida)

    PubMed Central

    Elshishka, Milka; Lazarova, Stela; Radoslavov, Georgi; Hristov, Petar; Peneva, Vlada K.

    2015-01-01

    Abstract The taxonomic position of two antarctic dorylaimid species Amblydorylaimus isokaryon (Loof, 1975) Andrssy, 1998 and Pararhyssocolpus paradoxus (Loof, 1975), gen. n., comb. n. are discussed on the basis of morphological, including SEM study, morphometric, postembryonic and sequence data of 18S rDNA and the D2-D3 expansion fragments of large subunit rDNA. The evolutionary trees inferred from 18S sequences show insufficient resolution to determine the assignment of the two species to particular families, moreover Pararhyssocolpus paradoxus gen. n., comb. n. (=Rhyssocolpus paradoxus) previously regarded as a member of Nordiidae or Qudsianematidae, showed distant relationship both to Rhyssocolpus vinciguerrae and Eudorylaimus spp. The phylogram inferred from 28S sequences revealed that Amblydorylaimus isokaryon is a member of a well-supported group comprised of several Aporcelaimellus spp., while, no close relationships could be revealed for the Pararhyssocolpus paradoxus gen. n., comb. n. to any nematode genus. On the basis of molecular data and morphological characteristics, some taxonomic changes are proposed. Amblydorylaimus isokaryon is transferred from family Qudsianematidae to family Aporcelaimidae, and a new monotypic genus Pararhyssocolpus gen. n. is proposed, attributed to Pararhyssocolpidae fam. n. The diagnosis of the new family is provided together with emended diagnosis of the genera Amblydorylaimus and Pararhyssocolpus gen. n. Data concerning distribution of these endemic genera in the Antarctic region are also given. PMID:26257550

  13. Visual Advantage of Enhanced Flight Vision System During NextGen Flight Test Evaluation

    NASA Technical Reports Server (NTRS)

    Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K.

    2014-01-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

  14. Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake

    PubMed Central

    Hahn, Martin W.; Kasalick, Vojt?ch; Jezbera, Jan; Brandt, Ulrike; Jezberov, Jitka; imek, Karel

    2011-01-01

    The chemoorganotrophic, aerobic, facultatively anaerobic, non-motile strain MWH-C5T isolated from the water column of oligo-mesotrophic Lake Mondsee (Austria) was phenotypically, phylogenetically, and chemotaxonomically characterized. The predominant fatty acids of the strain were C16:1?7c/?6c, C16:0, C12:1, and C8:0-3OH, the major quinone was ubiquinone Q-8, and the G+C content of the DNA of the strain was 55.5 mol%. The 16S rRNA gene similarity to the closest related type species were 96.6% (Curvibacter delicatus) and 95.7% (Rhodoferax fermentans). The phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of the strain with the family Comamonadaceae (Betaproteobacteria), however, the revealed phylogenetic position of the strain did not indicate the affiliation to any previously described genus within this family. A family-wide comparison of traits revealed that the strain possesses a unique combination of G+C value, major fatty acids, and major 3-hydroxy fatty acid. Furthermore, the strain differs in several traits from the closest related genera. Based on the phylogeny of the strain and the differences to the closest related genera, we propose to establish the genus Limnohabitans gen. nov. to accommodate this strain, and to place the strain in the new species Limnohabitans curvus sp. nov., with the type strain MWH-C5T (DSM 21645T, = CCUG 56720 T). The type strain is closely related to a large number of uncultured bacteria detected by cultivation-independent methods in various freshwater systems. PMID:19671731

  15. Mumia flava gen. nov., sp. nov., an actinobacterium of the family Nocardioidaceae.

    PubMed

    Lee, Learn-Han; Zainal, Nurullhudda; Azman, Adzzie-Shazleen; Mutalib, Nurul-Syakima Ab; Hong, Kui; Chan, Kok-Gan

    2014-05-01

    A novel actinobacterial strain, designated MUSC 201T, was isolated from a mangrove soil collected from Kuantan, the capital city of Pahang State in Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 201T represented a novel lineage within the class Actinobacteria. Strain MUSC 201T formed a distinct clade in the family Nocardioidaceae and was most closely related to the members of the genera Nocardioides (16S rRNA gene sequence similarity, 91.9-95.1%), Aeromicrobium (92.7-94.6%), Marmoricola (92.5-93.1%) and Kribbella (91.5-92.4%). The cells of this strain were irregular coccoid to short rod shaped. The peptidoglycan contained ll-diaminopimelic acid as diagnostic diamino acid and the peptidoglycan type was A3γ. The peptidoglycan cell wall contained ll-diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio of 1.5:0.9:1.0:1.5. The cell-wall sugars were galactose and rhamnose. The predominant menaquinone was MK-9(H4). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipid, glycolipid and four unknown phospholipids. The major cellular fatty acids were C18:1ω9c (30.8%), C16:0 (24.1%), and 10-methyl C18:0 (13.9%). The DNA G+C content was 72.0±0.1 mol%. On the basis of phylogenetic and phenotypic differences from members of the genera of the family Nocardioidaceae, a novel genus and species, Mumia flava gen. nov., sp. nov. are proposed. The type strain of Mumia flava is MUSC 201T (=DSM 27763T=MCCC 1A00646T=NBRC 109973T). PMID:24449791

  16. Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis

    NASA Technical Reports Server (NTRS)

    Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Matsa, M. E.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1995-01-01

    An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion.

  17. Description of Laccomimus gen. n. and eleven new species from the Neotropical region (Coleoptera, Dytiscidae, Laccophilinae).

    PubMed

    Toledo, Mario; Michat, Mariano C

    2015-01-01

    A new genus of laccophiline diving beetles, Laccomimus gen. n., is here described on the basis of a large number of specimens from various collections formerly misidentified as members of the Neotropical genus Laccodytes Rgimbart, 1895. Except for similar size, however, the new genus is not closely related to Laccodytes. Instead, it seems to be sister to the Oriental genus Laccosternus Brancucci, 1983, both sharing a similar body size and shape, characters of the female genital structures, and shape of the prosternal process. Twelve species are recognised within Laccomimus, all new to science except Laccomimus pumilio (LeConte, 1878) comb. n., the type species. The new species are: Laccomimus alvarengi sp. n., L. amazonas sp. n., L. bolivari sp. n., L. bordoni sp. n., L. distinctus sp. n., L. improvidus sp. n., L. malkini sp. n., L. spangleri sp. n., L. spinosus sp. n., L. variegatus sp. n., L. youngi sp. n. The distribution of the new genus includes most of the Neotropics, with one species, L. pumilio, reaching Florida, USA. Each taxon is described and illustrated and a key for their identification is provided. Laccomimus is a widespread and relatively common genus in tropical America, the species of which have a wide distributional range, except for a few confined to more restricted areas. In spite of this, Laccomimus is a very uniform genus in body shape, size and colouration, and in most cases identification of the species is possible only after examination of the male genitalia. A key to distinguish genera of the tribe Laccophilini is also presented. PMID:26250237

  18. Sulfuricaulis limicola gen. nov., sp. nov., a sulfur oxidizer isolated from a lake.

    PubMed

    Kojima, Hisaya; Watanabe, Tomohiro; Fukui, Manabu

    2016-01-01

    A novel sulfur-oxidizing bacterium, strain HA5T, was isolated from sediment of a lake in Japan. The cells were rod-shaped (0.3-0.5 × 1.2-6.0 μm) and Gram-stain-negative. The G+C content of the genomic DNA was 63 mol%. The major components in the cellular fatty acid profile were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The strain oxidized thiosulfate, tetrathionate and elemental sulfur as electron donors to support autotrophic growth. Growth was observed at a temperature range of 8-37 °C, with optimum growth at 28-32 °C. The pH range for growth was pH 6.1-9.2. Optimum growth of the isolate was observed in medium without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Acidiferrobacteraceae in the class Gammaproteobacteria. The closest relative was Sulfurifustis variabilis skN76T with the highest 16S rRNA gene sequence similarity of 93 %. On the basis of phylogenetic and phenotypic properties, strain HA5T is proposed to represent a novel species of a new genus, Sulfuricaulis limicola gen. nov., sp. nov. The type strain of the type species is HA5T ( = DSM 100373T = NBRC 110752T). PMID:26503693

  19. Lacimonas salitolerans gen. nov., sp. nov., isolated from surface water of a saline lake.

    PubMed

    Zhong, Zhi-Ping; Liu, Ying; Wang, Fang; Zhou, Yu-Guang; Liu, Hong-Can; Liu, Zhi-Pei

    2015-12-01

    A Gram-stain-negative bacterium, strain TS-T30T, was isolated from a saline lake (Lake Tuosu) in Qaidam basin, Qinghai province, China, and its taxonomic position was determined by using a polyphasic approach. Cells were non-spore-forming rods, non-motile, 0.8-1.4??m wide and 1.9-4.0??m long. Strain TS-T30T was strictly heterotrophic and aerobic. Catalase- and oxidase-positive. Growth was observed in the presence of 0.5-11.0?% (w/v) NaCl (optimum 3.0?%), and at 10-35?C (optimum 25?C) and pH?6.5-10.0 (optimum pH?8.5). Strain TS-T30T contained C18?:?1?7c as the only predominant fatty acid. The major respiratory quinone was Q-10. The DNA G+C content was 62?mol% (Tm). Phylogenetic trees based on 16S rRNA gene sequences showed that strain TS-T30T formed a distinct lineage that was independent of other most closely related genera: Lutimaribacter (95.2-95.9?% 16S rRNA gene sequence similarities), Poseidonocella (95.4?%), Ruegeria (92.8-94.9?%), Marivita (93.6-94.9?%), Seohaeicola (94.7?%), Sediminimonas (94.7?%), Shimia (93.9-94.7?%), Oceanicola (92.6-94.5?%) and Roseicyclus (94.5?%). The major polar lipids were phosphatidylglycerol, one unidentified phospholipid and an unknown aminolipid; phosphatidylcholine was not detected. These data demonstrated that strain TS-T30T represents a novel species of a new genus in the family Rhodobacteraceae, for which the name Lacimonas salitolerans gen. nov., sp. nov. is proposed. The type strain of the type species is TS-T30T (?=?CGMCC 1.12477T?=?NBRC 110969T). PMID:26373783

  20. Canaleparolina darwiniensis, gen. nov., sp. nov., and other pillotinaceous spirochetes from insects.

    PubMed

    Wier, A; Ashen, J; Margulis, L

    2000-12-01

    We describe two new pillotinaceous spirochetes (Canaleparolina darwiniensis, Diplocalyx cryptotermitidis) and identify for the first time Hollandina pterotermitidis from both the subterranean termite Cryptotermes cavifrons and the wood-eating cockroach Cryptocercus punctulatus based on morphometric analysis of transmission electron micrographic thin sections. C. darwiniensis, gen. nov., sp. nov., limited to near Darwin, Australia, invariably is present on the surface of the treponeme-studded trichomonad Mixotricha paradoxa, a consistent inhabitant of the hindgut of healthy termite Mastotermes darwiniensis. The spirochete both attached to the surface of protists and free-swimming in the paunch (hindgut) lumen of the insect has 16 periplasmic flagella (16:32:16) and imbricated wall structures that resemble flattened crenulations of Pillotina. The flagella surround half the protoplasmic cylinder. C. darwiniensis is the largest (0.5 microm diameter x 25 microm length) of the three epibiotic bacteria (two spirochetes, one rod) that comprise the complex cortex of its host Mixotricha paradoxa. Several criteria distinguish Diplocalyx cryptotermitidis sp. nov. isolated from Cryptotermes cavifrons intestine: smaller diameter, fewer flagella, absence of inner and outer coats of the outer membrane, wider angle subtended by its flagella and, most notably, cytoplasmic tubule-associated centers, which are periodic electron dense spheres within the protoplasmic cylinder from which emanate cytoplasmic tubules up to 24 nm in diameter. This is also the first report of abundant populations of Hollandina in Cryptotermes cavifrons (those populations belong to the species H. pterotermitidis). Morphometric analysis of the first thin sections of any spirochetes (published nearly 40 years ago by A.V. Grimstone) permits us to identify the large (0.9 microm diameter) free-swimming intestinal symbiont of Cryptocercus punctulatus also as Hollandina pterotermitidis. PMID:11334304

  1. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.

    PubMed

    Derrien, Muriel; Vaughan, Elaine E; Plugge, Caroline M; de Vos, Willem M

    2004-09-01

    The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G + C content of DNA from strain MucT was 47.6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (= ATCC BAA-835T = CIP 107961T). PMID:15388697

  2. Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano.

    PubMed

    Pikuta, Elena V; Hoover, Richard B; Marsic, Damien; Whitman, William B; Lupa, Boguslaw; Tang, Jane; Krader, Paul

    2009-09-01

    A novel, obligately anaerobic, psychrotolerant bacterium, designated strain PPP2T, was isolated from guano of the Magellanic penguin (Spheniscus magellanicus) in Chilean Patagonia. Cells were Gram-stain-positive, spore-forming, straight rods (0.7-0.8x3.0-5.0 microm) that were motile by means of peritrichous flagella. Growth was observed at pH 6.7-9.7 (optimum pH 8.3) and 2-37 degrees C (optimum 29 degrees C). Growth was observed between 0 and 4% (w/v) NaCl with optimum growth at 0.5% (w/v). Strain PPP2T was a catalase-negative chemo-organoheterotroph that was capable of fermentative metabolism. Peptone, bacto-tryptone, Casamino acids, oxalate, starch, chitin and yeast extract were utilized as substrates. The major metabolic products were acetate, butyrate and ethanol. Strain PPP2T was resistant to ampicillin, but sensitive to tetracycline, chloramphenicol, rifampicin, kanamycin, vancomycin and gentamicin. The DNA G+C content of strain PPP2T was 39.5 mol%. Phylogenetic analysis revealed that strain PPP2T was related most closely to Clostridium sticklandii SR (approximately 90% 16S rRNA gene sequence similarity). On the basis of phylogenetic analysis and phenotypic characteristics, strain PPP2T is considered to represent a novel species of a new genus, for which the name Proteocatella sphenisci gen. nov., sp. nov. is proposed. The type strain of Proteocatella sphenisci is PPP2T (=ATCC BAA-755T=JCM 12175T=CIP 108034T). PMID:19620379

  3. Haloactinospora alba gen. nov., sp. nov., a halophilic filamentous actinomycete of the family Nocardiopsaceae.

    PubMed

    Tang, Shu-Kun; Tian, Xin-Peng; Zhi, Xiao-Yang; Cai, Man; Wu, Jin-Yuan; Yang, Ling-Ling; Xu, Li-Hua; Li, Wen-Jun

    2008-09-01

    A novel halophilic, filamentous, actinomycete strain, designated YIM 90648(T), was isolated from a salt lake in Xinjiang Province, north-west China, and subjected to a polyphasic taxonomic study. Optimal growth occurred at 37 degrees C, pH 7.0-8.0 and 15% (w/v) NaCl. The aerial mycelium of strain YIM 90648(T) formed long chains of spores at maturity and the spores were cylindrical with smooth surfaces. Spore chains with pseudosporangia at the end were borne on the substrate mycelium and most spores had wrinkled surfaces. Strain YIM 90648(T) contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and ribose as the major whole-cell components. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and phosphatidylinositol mannoside. MK-10(H(8)), MK-11(H(4)), MK-11(H(6)) and MK-11(H(8)) were the predominant menaquinones. The major fatty acids were i-C(16:0) and ai-C(17:0). The DNA G+C content was 68 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 90648(T) formed a distinct lineage within the family Nocardiopsaceae and showed 16S rRNA gene sequence similarity of 93.3-95.0% with members of the family Nocardiopsaceae. On the basis of the polyphasic evidence, a novel genus and species, Haloactinospora alba gen. nov., sp. nov., is proposed to accommodate this isolate. The type strain of Haloactinospora alba is YIM 90648(T) (=DSM 45015(T) =CCTCC AA 206008(T)). PMID:18768607

  4. Halovarius luteus gen. nov., sp. nov., an extremely halophilic archaeon from a salt lake.

    PubMed

    Mehrshad, Maliheh; Amoozegar, Mohammad Ali; Makhdoumi, Ali; Rasooli, Mehrnoosh; Asadi, Basaer; Schumann, Peter; Ventosa, Antonio

    2015-08-01

    An extremely halophilic archaeon, strain DA50T, was isolated from a brine sample of Urmia lake, a hypersaline environment in north-west Iran. Strain DA50T was orange-pigmented, motile, pleomorphic and required at least 2.5?M NaCl but not MgCl2 for growth. Optimal growth was achieved at 4.0?M NaCl and 0.3?M MgCl2. The optimum pH and temperature for growth were pH?7.0 and 45?C, while it was able to grow over a pH range of 6.5-8.0 and a temperature range of 25-50?C. Analysis of 16S rRNA gene sequences revealed that strain DA50T is a member of the family Halobacteriaceae, showing a low level of similarity with other members of this family. Highest similarities, 94.4, 94.0 and 93.9?%, were obtained with the 16S rRNA gene sequences of the type strains of Natrialba aegyptia, Halobiforma lacisalsi and Halovivax asiaticus, respectively. Polar lipid analyses revealed that strain DA50T contains phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. Four unidentified glycolipids and two minor phospholipids were also observed. The only quinone present was MK-8(II-H2). The G+C content of its DNA was 62.3?mol%. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain DA50T is thus considered to represent a novel species of a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halovarius luteus gen. nov., sp. nov. is proposed. The type strain of Halovarius luteus is DA50T (?=?IBRC-M 10912T?=?CECT 8510T). PMID:25899505

  5. Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov.

    PubMed

    Nicklas, Werner; Bisgaard, Magne; Aalbk, Bent; Kuhnert, Peter; Christensen, Henrik

    2015-10-01

    To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2?% for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9?%, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was 'Haemophilus influenzae-murium', with 88.4?% similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from (?-?)-d-mannitol and hydrolysis of aesculin are variable, while the ?-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14?:?0, C14?:?0 3-OH/iso-C16?:?1 I, C16?:?1?7c and C16?:?0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T (?=?NCTC 12432T?=?ATCC 49577T). PMID:26296776

  6. Pseudogulbenkiania subflava gen. nov., sp. nov., isolated from a cold spring.

    PubMed

    Lin, Mei-Chun; Chou, Jui-Hsing; Arun, A B; Young, Chiu-Chung; Chen, Wen-Ming

    2008-10-01

    A yellow-coloured bacterial strain, designated BP-5(T), was isolated from a water sample of a cold spring located in the Hsinchu area of northern Taiwan. Cells of the strain were Gram-negative, non-spore-forming rods with a polar flagellum. The isolate was able to grow at 15-42 degrees C, 0-1 % NaCl and pH 6-8. The predominant fatty acids were summed feature 3 (C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH), C(16 : 0) and C(18 : 1)omega7c. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 63.2 mol%. 16S rRNA gene sequence analysis indicated that strain BP-5(T) belonged to the class Betaproteobacteria and was a member of the family Neisseriaceae. Its closest phylogenetic neighbours were Gulbenkiania mobilis E4FC31(T) (95.0 % 16S rRNA gene sequence similarity), Chromobacterium subtsugae PRAA4-1(T) (95.0 %), Chromobacterium violaceum ATCC 12472(T) (94.3 %), Vogesella indigofera ATCC 19706(T) (93.8 %) and Aquitalea magnusonii TRO-001DR8(T) (93.7 %). On the basis of the evidence from this polyphasic study, strain BP-5(T) is considered to represent a novel species of a new genus, for which the name Pseudogulbenkiania subflava gen. nov., sp. nov. is proposed. The type strain of Pseudogulbenkiania subflava is BP-5(T) (=BCRC 17727(T) =LMG 24211(T)). PMID:18842860

  7. Marimicrobium arenosum gen. nov., sp. nov., a moderately halophilic bacterium isolated from sea sand.

    PubMed

    Konkit, Maytiya; Kim, Jong-Hwa; Kim, Wonyong

    2016-02-01

    A Gram-stain-negative, non-pigmented, non-spore-forming, non-motile, strictly aerobic bacterial strain, designated CAU 1038T, was isolated from a sea sand sample in Modo, Republic of Korea, and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1038T grew optimally at 30 °C, pH 7.5 in 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1038T formed a distinct lineage within the class Gammaproteobacteria as a separate deep branch, with 95.2 % or lower sequence similarity to representatives of the genera Haliea, Halioglobus and Chromatocurvus, and 92.3 % or lower with Luminiphilus, Pseudohaliea and Congregibacter. The major cellular fatty acids of strain CAU 1038T were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The polar lipid pattern of the isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The strain contained lipoquinone (Q-8) as the sole respiratory quinone. The G+C content of the genomic DNA was 65 mol%. On the basis of phenotypic and chemotaxonomic data, and phylogenetic inference, strain CAU 1038T represents a novel species of a new genus in the family Halieaceae, for which the name Marimicrobium arenosum gen. nov., sp. nov. is proposed. The type strain of the type species is CAU 1038T ( = KCTC 42300T = NBRC 110727T). PMID:26611676

  8. Halotia gen. nov., a phylogenetically and physiologically coherent cyanobacterial genus isolated from marine coastal environments.

    PubMed

    Genuário, Diego Bonaldo; Vaz, Marcelo Gomes Marçal Vieira; Hentschke, Guilherme Scotta; Sant'Anna, Célia Leite; Fiore, Marli Fátima

    2015-02-01

    Nostoc is a common and well-studied genus of cyanobacteria and, according to molecular phylogeny, is a polyphyletic group. Therefore, revisions of this genus are urged in an attempt to clarify its taxonomy. Novel strains isolated from underexplored environments and assigned morphologically to the genus Nostoc are not genetically related to the 'true Nostoc' group. In this study, four strains isolated from biofilms collected in Antarctica and five strains originated from Brazilian mangroves were evaluated. Despite their morphological similarities to other morphotypes of Nostoc, these nine strains differed from other morphotypes in ecological, physiological and genetic aspects. Based on the phylogeny of the 16S rRNA gene, the Antarctic sequences were grouped together with the sequences of the Brazilian mangrove isolates and Nostoc sp. Mollenhauer 1 : 1-067 in a well-supported cluster (74 % bootstrap value, maximum-likelihood). This novel cluster was separated phylogenetically from the 'true Nostoc' clade and from the clades of the morphologically similar genera Mojavia and Desmonostoc. The 16S rRNA gene sequences generated in this study exhibited 96 % similarity to sequences from the nostocacean genera mentioned above. Physiologically, these nine strains showed the capacity to grow in a salinity range of 1-10 % NaCl, indicating their tolerance of saline conditions. These results provide support for the description of a new genus, named Halotia gen. nov., which is related morphologically to the genera Nostoc, Mojavia and Desmonostoc. Within this new genus, three novel species were recognized and described based on morphology and internal transcribed spacer secondary structures: Halotia branconii sp. nov., Halotia longispora sp. nov. and Halotia wernerae sp. nov., under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants. PMID:25424485

  9. Pharmacogenetic effects of candidate gene complexes on stroke in the GenHAT study

    PubMed Central

    Srensen, Izel F.; Vazquez, Ana I.; Irvin, Marguerite R.; Srensen, Peter; Davis, Barry R.; Ford, Charles E.; Boerwinkle, Eric; Eckfeldt, John H.; Arnett, Donna K.

    2014-01-01

    Objective The goal of this study was to investigate whether there is a genotype by treatment interaction in patients experiencing stroke and treated with one of three antihypertensive drugs, i.e. chlorthalidone, amlodipine and lisinopril. Methods A population of 436 African Americans and 539 whites that have experienced stroke in the GenHAT study were genotyped for 768 single nucleotide polymorphisms in 280 candidate genes. To detect a genotype by treatment interaction we used the Pearson's chi-square test to assess if the genotype frequencies differed at the single SNP level for the three drug treatment groups. From these single SNP analyses we derived a summary statistic for the degree of association at the gene and gene complex levels. This was done by grouping SNPs using information on gene locations and defining gene complexes based on protein-protein interactions. To assess the statistical significance of the observed test statistic we derived an empirical p-value by simulating data under the null hypothesis. Results We found that, in patients that have experienced stroke, there is a significant genetic difference between hypertension drug treatment groups. In African Americans SNP rs12143842 showed significant association (p < 0.001) with drug treatment. At gene-level HNRNPA1P4 and NOS1AP in African Americans and PRICKLE1 and NINJ2 in non-Hispanic whites were significantly associated (p < 0.01) to drug treatment, while none of the gene-complexes tested showed significance. Conclusions Based on the genetic differences between drug treatment groups, we conclude that there may be an interaction between certain genotypes and antihypertensive treatment in stroke patients. This needs to be replicated in other studies. PMID:25171760

  10. Evaluation of the Gen-Probe DNA probe for the detection of legionellae in culture.

    PubMed Central

    Edelstein, P H

    1986-01-01

    A commercial DNA probe kit designed to detect rRNA from legionellae was evaluated for its ability to correctly discriminate between legionellae and non-legionellae taken from culture plates. The probe kit, made by the Gen-Probe Corp. (San Diego, Calif.), was radiolabeled with 125I, and probe bacterial RNA hybridization, detected in a simple one-tube system hybridization assay, was quantitated with a gamma counter. A total of 156 Legionella sp. strains were tested, of which 125 were Legionella pneumophila and the remainder were strains from 21 other Legionella spp. A total of 106 gram-negative non-legionellae, isolated from human respiratory tract (81%) and other body site (19%) specimens, were also tested; 14 genera and 28 species were represented. The probe easily distinguished all of the legionellae from the non-legionellae. The average legionellae/non-legionellae hybridization ratio was 42:1, and the lowest ratio was 2:1; a minor modification in the procedure increased the lowest ratio to 5:1. In addition to correctly identifying all Legionella species, the probe was able to separate some of the various species of Legionella. L. pneumophila strains hybridized more completely to the probe than did the other Legionella spp.; L. wadsworthii and L. oakridgensis hybridized only about 25% of the probe relative to L. pneumophila. Some strains of phenotypically identified L. pneumophila had much lower hybridization to the probe than other members of the species and may represent a new Legionella species. The simplicity of the technique and specificity of the probe make it a good candidate for confirming the identity of legionellae in culture. PMID:2420820

  11. Analysis of first proximity voltage on the property of GEN ? image intensifier

    NASA Astrophysics Data System (ADS)

    Zhang, Ni; Zhu, Yu-feng; Li, Dan; Nie, Jing; Zhang, Tai-min; Liu, Xiao-jian; Liu, Zhao-lu; Cheng, Wei; Fu, Ling-yun

    2013-08-01

    First proximity voltage is the voltage between the cathode of Low Light Level image intensifier and the input surface of Micro-channel plate?MCP?. There are so many factors influencing the image intensifier performance, and the first proximity voltage is one of the most important factors that can not be ignored. Based on the theory analysis and test of different proximity voltage on the gain?signal-to-noise ratio and equivalent background noise, this test has studied on the important performance of Gen III image intensifier effected by the proximity voltage. By the experimental study, the increase of first proximity voltage to a certain extent can improve gain?signal-to-noise ratio and equivalent background noise at the same time. The main cause of this phenomenon is that the increase of proximity voltage can enlarge the incident electron energy, and then improve the quantum efficiency of the incident electron; meantime, stray electron produced by field emission at the action of the electric field of filmed-MCP will lead to equivalent background deterioration. Ultimately we conclude that: 1) Signal to noise is proportional to the square of he cathode sensitivity, increases with the first collision energy of the incident electron, especially at 200-500ev. 2)In the increasing process of voltage from 300v to 800v, the gain of filmed-MCP increases rapidly, but lower again when Upk increases further because of gain self-saturation; lgG and lgUpk are linear relationship, thus the curve can intuitively demonstrate the relationship between them. 3) Stray electron produced by field emission at the action of the electric field of filmed-MCP will lead to equivalent background deterioration, but will not exceed the requirements of technical specifications?2.510-7lx?.

  12. Halonotius pteroides gen. nov., sp. nov., an extremely halophilic archaeon recovered from a saltern crystallizer.

    PubMed

    Burns, David G; Janssen, Peter H; Itoh, Takashi; Kamekura, Masahiro; Echigo, Akinobu; Dyall-Smith, Mike L

    2010-05-01

    Strains 1.15.5(T), 2.27.5, 5.24.4 and 6.14.5 were isolated from a solar saltern. They have flattened, rod-shaped cells and are aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media around neutral pH and containing 20-24 % (w/v) (strains 1.15.5(T) and 2.27.5) or 22-24 % (w/v) (5.24.4 and 6.14.5) salts. Mg(2+) was not required. The DNA G+C contents of these isolates were all close to 58 mol%, and DNA-DNA cross-hybridization showed a mean relatedness of 77 %. Their 16S rRNA gene sequences differed by no more than 1.6 % from each other. Phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halorubrum saccharovorum (86.6-87.6 % 16S rRNA gene sequence similarity to the type strain). The only major polar lipid of all four isolates was the sulfated diglycosyl diether lipid S-DGD-1. By phase-contrast microscopy, the long, flattened cells of these strains often displayed a 'wing-like' shape. The phenotypic and phylogenetic data support the placement of these isolates into a novel species in a new genus within the Halobacteriaceae, for which we propose the name Halonotius pteroides gen. nov., sp. nov. The type strain of Halonotius pteroides is 1.15.5(T) (=JCM 14355(T) =CECT 7525(T) =DSM 18729(T)), with the additional reference strains 2.27.5 (=JCM 14356 =DSM 18671), 5.24.4 (=JCM 14357 =DSM 18673) and 6.14.5 (=JCM 14358 =DSM 18692). PMID:19667389

  13. Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae.

    PubMed

    Zhou, En-Min; Yu, Tian-Tian; Liu, Lan; Ming, Hong; Yin, Yi-Rui; Dong, Lei; Tseng, Min; Nie, Guo-Xing; Li, Wen-Jun

    2014-09-01

    Strains YIM 77562(T) and YIM 77580, two novel Gram-staining-positive, filamentous bacterial isolates, were recovered from the Rehai geothermal field, Tengchong, Yunnan province, south-west China. Good growth was observed at 50-55 C and pH 7.0. Aerial mycelium was absent on all media tested. Substrate mycelium was well-developed, long and moderately flexuous, and formed abundant, single, warty, ornamented endospores. Phylogenetic analysis of the 16S rRNA gene sequences of the two strains indicated that they belong to the family Thermoactinomycetaceae. Similarity levels between the 16S rRNA gene sequences of the two strains and those of type strains of members of the Thermoactinomycetaceae were 88.33-93.24?%; the highest sequence similarity was with Hazenella coriacea DSM 45707(T). In both strains, the predominant menaquinone was MK-7, the diagnostic diamino acid was meso-diaminopimelic acid and the major cellular fatty acids were iso-C14?:?0, iso-C15?:?0 and iso-C16?:?0. The major polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids and unidentified phospholipids. The genomic DNA G+C contents of strains YIM 77562(T) and YIM 77580 were 45.5 and 44.2 mol%, respectively. DNA-DNA relatedness data suggest that the two isolates represent a single species. Based on phylogenetic analyses and physiological and biochemical characteristics, it is proposed that the two strains represent a single novel species in a new genus, Geothermomicrobium terrae gen. nov., sp. nov. The type strain of Geothermomicrobium terrae is YIM 77562(T) (?=?CCTCC AA 2011022(T)?=?JCM 18057(T)). PMID:24907264

  14. Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium.

    PubMed

    Tank, Marcus; Bryant, Donald A

    2015-05-01

    A novel anoxygenic photoheterotrophic member of the phylum Acidobacteria , Chloracidobacterium thermophilum strain B sp. nov., was isolated from a cyanobacterial enrichment culture derived from microbial mats associated with Octopus Spring, Yellowstone National Park, WY. C. thermophilum sp. nov. was a Gram-stain-negative rod (diameter, approximately 0.8-1.0 µm; variable length, approximately 2.5 µm), which formed greenish-brown liquid suspension cultures. It was a moderately thermophilic microaerophile and grew in a defined medium at 51 °C (T(opt); range 44 to 58 °C) and in the pH range 5.5 to 9.5 (pH(opt) = ~7.0). The DNA G+C content was 61.3 mol%, and phylogenetic analysis, based on the 16S rRNA sequence, showed that C. thermophilum sp. nov. belongs to subdivision 4 ( Acidobacteriaceae ) of the Acidobacteria . C. thermophilum sp. nov. was unable to synthesize branched-chain amino acids, L-lysine, and vitamin B12, which were required for growth. Although the organism lacked genes/enzymes for autotrophic carbon fixation, bicarbonate was required. Growth was stimulated by other amino acids and 2-oxoglutarate. Cells produced chlorosomes containing a diverse mixture of bacteriochlorophyll (BChl) c derivatives, and additionally, synthesized BChl a P, Chl a PD, and Zn-BChl a'P, which occurred in type-1 homodimeric reaction centres. The carotenoids included echinenone, canthaxanthin, lycopene, γ-carotene and β-carotene. C. thermophilum sp. nov. produced iso-diabolic acid as its major fatty acid and synthesized three hopanoids (diploptene, bacteriohopanetetrol and bacteriohopanetetrol cyclitol ether). Based upon its phenotypic and genotypic properties, the name Chloracidobacterium thermophilum gen. nov., sp. nov. is proposed for this isolate; the type strain is C. thermophilum strain B(T) (ATCC BAA-2647 = JCM 30199). PMID:25667398

  15. Alsobacter metallidurans gen. nov., sp. nov., a thallium-tolerant soil bacterium in the order Rhizobiales.

    PubMed

    Bao, Zhihua; Sato, Yoshinori; Fujimura, Reiko; Ohta, Hiroyuki

    2014-03-01

    A thallium-tolerant, aerobic bacterium, designated strain SK200a-9(T), isolated from a garden soil sample was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain SK200a-9(T) was affiliated with an uncultivated lineage within the Alphaproteobacteria and the nearest cultivated neighbours were bacteria in genera in the family Methylocystaceae (93.3-94.4% 16S rRNA gene sequence similarity) and the family Beijerinckiaceae (92.3-93.1%) in the order Rhizobiales. Cells of strain SK200a-9(T) were Gram-stain-negative, non-motile, non-spore-forming, poly-?-hydroxybutyrate-accumulating rods. The strain was a chemo-organotrophic bacterium, which was incapable of growth on C1 substrates. Catalase and oxidase were positive. Atmospheric nitrogen fixation and nitrate reduction were negative. The strain contained ubiquinone Q-10 and cellular fatty acids C18?:?1?7c, C18?:?0, C16?:?1?7c and C16?:?0 as predominant components. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content was 64.8 mol%. On the basis of the information described above, strain SK200a-9(T) is considered to represent a novel species of a new genus in the order Rhizobiales, for which the name Alsobacter metallidurans gen. nov., sp. nov. is proposed. The type strain of Alsobacter metallidurans is SK200a-9(T) (?=?NBRC 107718(T)?=?CGMCC 1.12214(T)). PMID:24221990

  16. Eoetvoesia caeni gen. nov., sp. nov., isolated from an activated sludge system treating coke plant effluent.

    PubMed

    Felföldi, Tamás; Vengring, Anita; Kéki, Zsuzsa; Márialigeti, Károly; Schumann, Peter; Tóth, Erika M

    2014-06-01

    A novel bacterium, PB3-7B(T), was isolated on phenol-supplemented inorganic growth medium from a laboratory-scale wastewater purification system that treated coke plant effluent. 16S rRNA gene sequence analysis revealed that strain PB3-7B(T) belonged to the family Alcaligenaceae and showed the highest pairwise sequence similarity to Parapusillimonas granuli Ch07(T) (97.5%), Candidimonas bauzanensis BZ59(T) (97.3%) and Pusillimonas noertemannii BN9(T) (97.2%). Strain PB3-7B(T) was rod-shaped, motile and oxidase- and catalase-positive. The predominant fatty acids were C(16 : 0), C(17 : 0) cyclo, C(19 : 0) cyclo ω8c and C(14 : 0) 3-OH, and the major respiratory quinone was Q-8. The G+C content of the genomic DNA of strain PB3-7B(T) was 59.7 mol%. The novel bacterium can be distinguished from closely related type strains based on its urease activity and the capacity for assimilation of glycerol and amygdalin. On the basis of the phenotypic, chemotaxonomic and molecular data, strain PB3-7B(T) is considered to represent a new genus and species, for which the name Eoetvoesia caeni gen. nov., sp. nov. is proposed. The type strain of Eoetvoesia caeni is PB3-7B(T) ( = DSM 25520(T) = NCAIM B 02512(T)). PMID:24585374

  17. 'Candidatus glomeribacter gigasporarum' gen. nov., sp. nov., an endosymbiont of arbuscular mycorrhizal fungi.

    PubMed

    Bianciotto, Valeria; Lumini, Erica; Bonfante, Paola; Vandamme, Peter

    2003-01-01

    Arbuscular mycorrhizal fungi are obligate endosymbionts that colonize the roots of almost 80 % of land plants. The present paper describes morphological and molecular data on a bacterial endosymbiont living in the cytoplasm of dormant or germinating spores and symbiotic mycelia of the fungal species Gigaspora margarita, Scutellospora persica and Scutellospora castanea. PCR amplification of almost the entire 16S rRNA gene of the Gigaspora margarita BEG 34 endosymbiont, using universal bacterial primers, and subsequent sequence analysis demonstrated that this organism occupies a very distinct phylogenetic position within the beta-Proteobacteria, with the genera Burkholderia, Pandoraea and Ralstonia as its closest neighbours. Primers specific to the 16S rDNA of the endosymbiotic bacteria of BEG 34 allowed amplification of spore DNA from endosymbionts of Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea, but not from the Gigaspora gigantea endosymbiont (which was morphologically different) or from the cytoplasm of Gigaspora rosea (which did not contain endosymbiotic bacteria). These specific primers were successfully used as a probe for the in-situ hybridization of endobacteria in Gigaspora margarita spores. The overall rod-shaped morphology of the Gigaspora margarita, Gigaspora decipiens, S. persica and S. castanea endosymbionts was similar, and amplification and sequence analysis of the almost-complete 16S rRNA genes of several Gigaspora margarita, S. persica and S. castanea endosymbionts revealed over 98% sequence similarity. These morphological and genomic characteristics were used to assign the endosymbionts of these three species (five isolates) of arbuscular mycorrhizal fungi as 'Candidatus Glomeribacter gigasporarum' gen. nov., sp. nov. PMID:12656162

  18. Visual advantage of enhanced flight vision system during NextGen flight test evaluation

    NASA Astrophysics Data System (ADS)

    Kramer, Lynda J.; Harrison, Stephanie J.; Bailey, Randall E.; Shelton, Kevin J.; Ellis, Kyle K. E.

    2014-06-01

    Synthetic Vision Systems and Enhanced Flight Vision System (SVS/EFVS) technologies have the potential to provide additional margins of safety for aircrew performance and enable operational improvements for low visibility operations in the terminal area environment. Simulation and flight tests were jointly sponsored by NASA's Aviation Safety Program, Vehicle Systems Safety Technology project and the Federal Aviation Administration (FAA) to evaluate potential safety and operational benefits of SVS/EFVS technologies in low visibility Next Generation Air Transportation System (NextGen) operations. The flight tests were conducted by a team of Honeywell, Gulfstream Aerospace Corporation and NASA personnel with the goal of obtaining pilot-in-the-loop test data for flight validation, verification, and demonstration of selected SVS/EFVS operational and system-level performance capabilities. Nine test flights were flown in Gulfstream's G450 flight test aircraft outfitted with the SVS/EFVS technologies under low visibility instrument meteorological conditions. Evaluation pilots flew 108 approaches in low visibility weather conditions (600 feet to 3600 feet reported visibility) under different obscurants (mist, fog, drizzle fog, frozen fog) and sky cover (broken, overcast). Flight test videos were evaluated at three different altitudes (decision altitude, 100 feet radar altitude, and touchdown) to determine the visual advantage afforded to the pilot using the EFVS/Forward-Looking InfraRed (FLIR) imagery compared to natural vision. Results indicate the EFVS provided a visual advantage of two to three times over that of the out-the-window (OTW) view. The EFVS allowed pilots to view the runway environment, specifically runway lights, before they would be able to OTW with natural vision.

  19. Algoriella xinjiangensis gen. nov., sp. nov., a new psychrotolerant bacterium of the family Flavobacteriaceae.

    PubMed

    Yang, Na; Zhang, Lixin; Sun, Chaomin

    2015-11-01

    An aerobic, Gram-stain negative, non-spore-forming and psychrotolerant bacterium, designated strain XJ109(T), was isolated from a sewage water sample collected from Xinjiang Uigur Autonomous Region, China. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain XJ109(T) represents a novel member of the family Flavobacteriaceae. The strain showed 95.5 % similarity with the 16S rRNA gene sequence of Empedobacter brevis LMG 4011(T), 95.4% with Chishuiella changwenlii BY4(T), 95.3% with Empedobacter falsenii NF 993(T) and 92.3% with Weeksella virosa DSM 16922(T). Strain XJ109(T) showed the common phenotypic and chemotaxonomic characteristics of the family Flavobacteriaceae, containing menaquinone-6 (MK-6) as the predominant respiratory quinone and iso-C17:0 3OH and iso-C15:0 as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one unidentified phospholipid and two unidentified lipids. The genomic DNA G+C content was 38.0 mol%. Strain XJ109(T) was positive for catalase and oxidase activities, and it was observed to grow at 4-30 C (optimal 16-20 C), pH 6.5-10.0 (optimal 7.0-7.5) and in media containing 0-2.0% (w/v) NaCl (optimal 0.5 %). On the basis of the polyphasic evidence presented, strain XJ109(T) is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Algoriella xinjiangensis gen. nov., sp. nov. is proposed. The type strain is XJ109(T) (=CGMCC 1.10229(T)=JCM 16590(T)). PMID:26310805

  20. Pseudohalocynthiibacter aestuariivivens gen. nov., sp. nov., isolated from a tidal flat.

    PubMed

    Won, Sung-Min; Park, Sooyeon; Park, Ji-Min; Kim, Byung-Chan; Yoon, Jung-Hoon

    2015-05-01

    A Gram-stain-negative, non-motile, aerobic and coccoid, ovoid or rod-shaped bacterial strain, designated BS-W9(T), was isolated from a tidal flat of the South Sea, South Korea. Strain BS-W9(T) grew optimally at 25-30 C, at pH 7.0-8.0 and in the presence of approximately 2.0% (w/v) NaCl. Phylogenetic trees, based on 16S rRNA gene sequences, revealed that strain BS-W9(T) clustered with the type strain of Halocynthiibacter namhaensis , showing a highest sequence similarity of 97.3%. It exhibited sequence similarity values of less than 95.6% to the type strains of other species with validly published names. Strain BS-W9(T) contained Q-10 as the predominant ubiquinone and C18:1?7c as the predominant fatty acid. The major polar lipids of strain BS-W9(T) were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The fatty acid and polar lipid profiles of strain BS-W9(T) were distinguished from those of the type strains of H. namhaensis and other phylogenetically related genera. The DNA G+C content of strain BS-W9(T) was 53.2 mol% and its mean DNA-DNA relatedness value with H. namhaensis RA2-3(T) was 14%. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain BS-W9(T) is considered to represent a novel genus and species within the family Rhodobacteraceae , for which the name Pseudohalocyntiibacter aestuariivivens gen. nov., sp. nov. is proposed. The type strain of Pseudohalocyntiibacter aestuariivivens is BS-W9(T) (?=KCTC 42348(T)?=CECT 8726(T)). PMID:25713042

  1. Thermus aquaticus gen. n. and sp. n., a Nonsporulating Extreme Thermophile

    PubMed Central

    Brock, Thomas D.; Freeze, Hudson

    1969-01-01

    The isolation of a new thermophilic bacterium, Thermus aquaticus gen. n. and sp. n., is described. Successful enrichment requires incubation at 70 to 75 C, and the use of nutrient media relatively dilute with respect to the organic components. Strains of T. aquaticus have been isolated from a variety of thermal springs in Yellowstone National Park and from a thermal spring in California. The organism has also been isolated from man-made thermal habitats, such as hot tap water, in geographical locations quite distant from thermal springs. Isolates of T. aquaticus are gram-negative nonsporulating nonmotile rods which frequently form long filaments at supraoptimal temperatures or in the stationary phase. All isolates form a yellow cellular pigment, probably a carotenoid. A characteristic structure formed by all isolates is a large sphere, considerably larger than a spheroplast. These large spheres, as well as lysozyme-induced spheroplasts, are resistant to osmotic lysis. Deoxyribonucleic acid base compositions of four strains were determined by CsCl density gradient ultracentrifugation and found to be between 65.4 and 67.4 moles per cent guanine plus cytosine. The growth of all isolates tested is inhibited by fairly low concentrations of cycloserine, streptomycin, penicillin, novobiocin, tetracycline, and chloramphenicol. Nutritional studies on one strain showed that it did not require vitamins or amino acids, although growth was considerably faster in enriched than in synthetic medium. Several sugars and organic acids served as carbon sources, and either NH4+ or glutamate could serve as nitrogen source. The organism is an obligate aerobe and has a pH optimum of 7.5 to 7.8. The optimum temperature for growth is 70 C, the maximum 79 C, and the minimum about 40 C. The generation time at the optimum is about 50 min. The possible relationships of this new genus to the myxobacteria, flexibacteria, and flavobacteria are discussed. Images PMID:5781580

  2. NextGen Flight Deck Surface Trajectory-Based Operations (STBO): Contingency Holds

    NASA Technical Reports Server (NTRS)

    Bakowski, Deborah Lee; Hooey, Becky Lee; Foyle, David C.; Wolter, Cynthia A.; Cheng, Lara W. S.

    2013-01-01

    The purpose of this pilot-in-the-loop taxi simulation was to investigate a NextGen Surface Trajectory-Based Operations (STBO) concept called "contingency holds." The contingency-hold concept parses a taxi route into segments, allowing an air traffic control (ATC) surface traffic management (STM) system to hold an aircraft when necessary for safety. Under nominal conditions, if the intersection or active runway crossing is clear, the hold is removed, allowing the aircraft to continue taxiing without slowing, thus improving taxi efficiency, while minimizing the excessive brake use, fuel burn, and emissions associated with stop-and-go taxi. However, when a potential traffic conflict exists, the hold remains in place as a fail-safe mechanism. In this departure operations simulation, the taxi clearance included a required time of arrival (RTA) to a specified intersection. The flight deck was equipped with speed-guidance avionics to aid the pilot in safely meeting the RTA. On two trials, the contingency hold was not released, and pilots were required to stop. On two trials the contingency hold was released 15 sec prior to the RTA, and on two trials the contingency hold was released 30 sec prior to the RTA. When the hold remained in place, all pilots complied with the hold. Results also showed that when the hold was released at 15-sec or 30-sec prior to the RTA, the 30-sec release allowed pilots to maintain nominal taxi speed, thus supporting continuous traffic flow; whereas, the 15-sec release did not. The contingency-hold concept, with at least a 30-sec release, allows pilots to improve taxiing efficiency by reducing braking, slowing, and stopping, but still maintains safety in that no pilots "busted" the clearance holds. Overall, the evidence suggests that the contingency-hold concept is a viable concept for optimizing efficiency while maintaining safety.

  3. Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae.

    PubMed

    Zhang, Gaiyun; Yang, Yanliu; Wang, Shuang; Sun, Zhilei; Jiao, Kailin

    2015-08-01

    A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4-50 °C, pH 6-11 and 0-10 % (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4%), followed by Ponticoccus litoralis CL-GR66T (96.4%), Antarctobacter heliothermus EL-219T (96.3%) and Thalassococcus lentus YCS-24T (96.0%). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 40.2%), anteiso-C15 : 0 (30.4%) and anteiso-C17 : 0 (9.7%). The genomic DNA G+C content of strain F15T was 60.2 mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T ( = LMG 28107T = JCM 19851T = CGMCC 1.12763T = MCCC 1A09948T). PMID:25908713

  4. Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring.

    PubMed

    Dong, Lei; Ming, Hong; Zhou, En-Min; Yin, Yi-Rui; Liu, Lan; Feng, Hui-Geng; Xian, Wen-Dong; Nie, Guo-Xing; Li, Wen-Jun

    2015-01-01

    A slightly thermophilic, Gram-staining-negative and strictly aerobic bacteria, designated strain YIM 78141(T), was isolated from a sediment sample collected at Hehua hot spring, Tengchong, Yunnan province, south-west China. Cells of the strain were short-rod-shaped and colonies were yellowish and circular. The strain grew at pH 6.0-10.0 (optimum, pH 8.0-9.0) and 10-55 C (optimum, 40-50 C). Phylogenetic analyses based on 16S rRNA gene sequence comparison demonstrated that strain YIM 78141(T) belongs to the family Neisseriaceae, and strain YIM 78141(T) also showed low levels of 16S rRNA gene sequence similarity (below 93.4%) with all other genera in this family. The only quinone was ubiquinone 8 and the genomic DNA G+C content was 67.3 mol%. Major fatty acids (>5%) were C12:0, C16:0, C18:1?7c and summed feature 3. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phospholipids of unknown structure containing aminoglycophospholipid and three unidentified polar lipids. On the basis of the morphological, physiological and biochemical characteristics as well as genotypic data, this strain should be classified as a representative of a novel genus and species of the family Neisseriaceae, for which the name Crenobacter luteus gen. nov., sp. nov. is proposed. The type strain is YIM 78141(T) (?=BCRC 80650(T)?=KCTC 32558(T)?=DSM 27258(T)). PMID:25332210

  5. Pseudorhodoplanes sinuspersici gen. nov., sp. nov., isolated from oil-contaminated soil.

    PubMed

    Tirandaz, Hassan; Dastgheib, Seyed Mohammad Mehdi; Amoozegar, Mohammad Ali; Shavandi, Mahmoud; de la Haba, Rafael R; Ventosa, Antonio

    2015-12-01

    Strain RIPI 110T was isolated from a soil sample collected from an oil-contaminated site on Siri Island, Persian Gulf, Iran. Cells of the novel isolate were Gram-stain-negative, facultatively anaerobic, non-motile and rod-shaped. Cells divided asymmetrically by budding and formed rosette-like clusters. The optimum pH and temperature for growth were pH 7 and 30 °C, while the strain was able to grow at pH 5.5-8 and 15-35 °C. Strain RIPI 110T utilized only complex carbon sources and pyruvate as the sole carbon source and could not grow under photoautotrophic conditions. The highest 16S rRNA gene sequence similarities, 93.9, 93.9 and 93.5 %, were obtained with Variibacter gotjawalensis GJW-30T, Rhodoplanes roseus 941T and Rhodoplanes elegans AS130T, respectively. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/ω6c), C16 : 0 and C19 : 0 cyclo ω8c. Polar lipid analyses revealed that strain RIPI 110T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid and four unknown phospholipids. Ubiquinone-10 was the predominant quinone component. The DNA G+C content was 59.4 mol%. On the basis of the 16S rRNA gene sequence analysis, in combination with chemotaxonomic and physiological data, the novel isolate could not be classified in any recognized genera. Strain RIPI 110T is thus considered to represent a novel species of a new genus within the order Rhizobiales, for which the name Pseudorhodoplanes sinuspersici gen. nov., sp. nov. is proposed. The type strain of the type species is RIPI 110T ( = IBRC-M 10770T = CECT 8374T). PMID:26420766

  6. Feasibility of a Networked Air Traffic Infrastructure Validation Environment for Advanced NextGen Concepts

    NASA Technical Reports Server (NTRS)

    McCormack, Michael J.; Gibson, Alec K.; Dennis, Noah E.; Underwood, Matthew C.; Miller,Lana B.; Ballin, Mark G.

    2013-01-01

    Abstract-Next Generation Air Transportation System (NextGen) applications reliant upon aircraft data links such as Automatic Dependent Surveillance-Broadcast (ADS-B) offer a sweeping modernization of the National Airspace System (NAS), but the aviation stakeholder community has not yet established a positive business case for equipage and message content standards remain in flux. It is necessary to transition promising Air Traffic Management (ATM) Concepts of Operations (ConOps) from simulation environments to full-scale flight tests in order to validate user benefits and solidify message standards. However, flight tests are prohibitively expensive and message standards for Commercial-off-the-Shelf (COTS) systems cannot support many advanced ConOps. It is therefore proposed to simulate future aircraft surveillance and communications equipage and employ an existing commercial data link to exchange data during dedicated flight tests. This capability, referred to as the Networked Air Traffic Infrastructure Validation Environment (NATIVE), would emulate aircraft data links such as ADS-B using in-flight Internet and easily-installed test equipment. By utilizing low-cost equipment that is easy to install and certify for testing, advanced ATM ConOps can be validated, message content standards can be solidified, and new standards can be established through full-scale flight trials without necessary or expensive equipage or extensive flight test preparation. This paper presents results of a feasibility study of the NATIVE concept. To determine requirements, six NATIVE design configurations were developed for two NASA ConOps that rely on ADS-B. The performance characteristics of three existing in-flight Internet services were investigated to determine whether performance is adequate to support the concept. Next, a study of requisite hardware and software was conducted to examine whether and how the NATIVE concept might be realized. Finally, to determine a business case, economic factors were evaluated and a preliminary cost-benefit analysis was performed.

  7. Flaviflexus huanghaiensis gen. nov., sp. nov., an actinobacterium of the family Actinomycetaceae.

    PubMed

    Du, Zong-Jun; Miao, Ting-Ting; Lin, Xue-Zheng; Liu, Qian-Qian; Chen, Guan-Jun

    2013-05-01

    Strain H5(T) was isolated from a sediment sample collected from the coastal area of Qingdao, China. The cells were Gram-stain-positive, non-motile, straight or curved rods. The temperature range for growth was 20-37 °C and the pH for growth ranged from 6.5 to 9.0, with optimum growth occurring in the temperature range 28-30 °C and pH range 7.5-8.0. Growth occurred in the presence of 0-6% (w/v) NaCl (optimum, 0-2%). Strain H5(T) had MK-9, MK-9(H2) and MK-9(H4) as the major menaquinones and C18:1ω9c, C16:0, C14:0, C18:0 and C16:1ω9c as major fatty acids. The cell-wall peptidoglycan type was A5α l-Lys-l-Ala-l-Lys-d-Glu. The major polar lipids were phosphatidylglycerol (PG), an unknown phospholipid (PL1) and two unknown phosphoglycolipids (PGL1, PGL2). An unknown phospholipid (PL2) and two unknown glycolipids (GL1, GL2) were present in moderate to minor amounts in the polar lipid profile. The genomic DNA G+C content was 61.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain H5(T) represents a novel lineage in the family Actinomycetaceae. On the basis of phenotypic, physiological and molecular characteristics, it is proposed that the novel isolate should be classified as a novel species in a new genus: Flaviflexus huanghaiensis gen. nov., sp. nov., with strain H5(T) ( = DSM 24315(T) =CICC 10486(T)) as the type strain of the type species. PMID:23002046

  8. Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae.

    PubMed

    Adachi, Kyoko; Katsuta, Atsuko; Matsuda, Satoru; Peng, Xue; Misawa, Norihiko; Shizuri, Yoshikazu; Kroppenstedt, Reiner M; Yokota, Akira; Kasai, Hiroaki

    2007-02-01

    A polyphasic taxonomic approach was applied to determine the taxonomic position of a hydrocarbon-degrading actinomycete, strain Hou_blueT, which was isolated from soil samples collected from an oil spring in Niigata, Japan. The results of 16S rRNA and gyrB gene sequence comparisons indicated that strain Hou_blueT represented a novel lineage in the suborder Corynebacterineae. Colonies were malachite green-like in colour on 1/10 trypticase soy agar and the cell morphology was coccoid in all growth phases. The cell-wall diamino acid and sugar indicated chemotype IV and variation A1gamma. The sugars of the peptidoglycan were glycolated. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and some unspecified glycolipids. The organism contained two novel cyclic forms of menaquinone, smaragdiquinone A-8(H4, omega-cycl) and smaragdiquinone B-8(H4, dicycl). The major fatty acids were cis-9-18 : 1 (34.46 %) and 16 : 0 (25.1 %). Small amounts of 10-methyl-branched fatty acids were also present (10-methyl-17 : 0, 0.17 %), but not tuberculostearic acid (10-methyl-18 : 0), which has been shown to be present in all nocardiae. Gas-chromatographic analysis of the mycolic acid revealed a carbon-chain length of C43-C49. The DNA G+C content was 63.7 mol%. On the basis of phenotypic and phylogenetic distinctness, the organism is proposed to represent a novel genus and species, Smaragdicoccus niigatensis gen. nov., sp. nov., with the type strain Hou_blueT (=MBIC 06267T=DSM 44881T). PMID:17267967

  9. Salinactinospora qingdaonensis gen. nov., sp. nov., a halophilic actinomycete isolated from a salt pond.

    PubMed

    Chang, Xianbo; Liu, Wenzheng; Zhang, Xiao-Hua

    2012-04-01

    A novel halophilic, filamentous, actinomycete strain, designated CXB832T, was isolated from a salt pond in Qingdao, China. Optimal growth occurred at 37 °C, pH 7.0-8.0 and 9-12 % (w/v) NaCl. Strain CXB832T formed pale yellow to deep yellow branched substrate mycelium without fragmentation. Abundant white aerial mycelium differentiated into long chains of spores and the spores were rod-shaped with smooth surfaces. Strain CXB832T contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell-wall peptidoglycan, and glucose and xylose as the major whole-cell sugars. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipids, glycolipid and unidentified lipids. MK-10(H8), MK-9(H8), MK-10(H2) and MK-10(H6) were the predominant menaquinones. The major fatty acids were i-C16:0 (30.71 %), ai-C17:0 (13.31 %) and C16:0 (11.28 %). The G+C content of the DNA was 60.1 mol%. Comparative analysis of 16S rRNA gene sequences showed that the novel strain was most closely related to genera within the family Nocardiopsaceae, but formed a separate lineage. The highest sequence similarities were to Nocardiopsis arabia DSM 45083T (95.4 %) and Haloactinospora alba DSM 45015T (94.9 %). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain CXB832T represents a new genus and novel species in the family Nocardiopsaceae, for which the name Salinactinospora qingdaonensis gen. nov., sp. nov. is proposed. The type strain of the type species is CXB832T (=DSM 45442T=LMG 25567T). PMID:21669918

  10. Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium.

    PubMed

    Lechner, Ute; Brodkorb, Danny; Geyer, Roland; Hause, Gerd; Hrtig, Claus; Auling, Georg; Fayolle-Guichard, Franoise; Piveteau, Pascal; Mller, Roland H; Rohwerder, Thore

    2007-06-01

    Strains L10(T), L108 and CIP I-2052 were originally obtained from methyl tert-butyl ether (MTBE)-contaminated groundwater and from a wastewater treatment plant, respectively. All share the ability to grow on tert-butanol, an intermediate of MTBE degradation. Cells are strictly aerobic, motile by a polar flagellum and exhibit strong pili formation. Poly beta-hydroxybutyrate (PHB) granules are formed. The DNA G+C content is 69-70.5 mol% and the main ubiquinone is Q-8. The major cellular fatty acids are 16 : 1 cis-9 and 16 : 0 and the only hydroxy fatty acid is 10 : 0 3-OH. The major phospholipids are phosphatidylethanolamine (PE) 16 : 1/16 : 1 and phosphatidylglycerol 16 : 0/16 : 1. A significant amount of PE 17 : 0/16 : 1 is present. The 16S rRNA gene sequences of these strains are almost identical and form a separate line of descent in the Rubrivivax-Roseateles-Leptothrix-Ideonella-Aquabacterium branch of the Betaproteobacteria with 97 % similarity to 16S rRNA genes of the type strains of Rubrivivax gelatinosus, Leptothrix mobilis and Ideonella dechloratans. However, physiological properties, DNA-DNA relatedness values and the phospholipid and cellular fatty acid profiles distinguish the novel isolates from the three closely related genera. Therefore, it is concluded that strains L10(T), L108 and CIP I-2052 represent a new genus and novel species for which the name Aquincola tertiaricarbonis gen. nov., sp. nov., is proposed. The type strain is strain L10(T) (=DSM 18512(T)=CIP 109243(T)). PMID:17551046

  11. Arcticiflavibacter luteus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from intertidal sand.

    PubMed

    Liu, Chang; Zhang, Xi-Ying; Wen, Xi-Ruo; Shi, Mei; Chen, Xiu-Lan; Su, Hai-Nan

    2016-01-01

    A yellow-pigmented, rod-shaped, non-flagellated, aerobic and Gram-reaction-negative bacterium, designated strain SM1212T, was isolated from intertidal sand of Kongsfjorden, Svalbard. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SM1212T constituted a distinct lineage within the family Flavobacteriaceae. It shared highest 16S rRNA gene sequence similarities with the type strains of Bizionia echini (96.0?%), Lacinutrix jangbogonensis (95.8?%) and Psychroserpens damuponensis (95.7?%) and gen. nov., sp. nov. is proposed. The type strain of Arcticiflavibacter luteus is SM1212T (?=?MCCC 1K00234T?=?KCTC 32514T). PMID:26475791

  12. Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis.

    PubMed

    Buldyrev, S V; Goldberger, A L; Havlin, S; Mantegna, R N; Matsa, M E; Peng, C K; Simons, M; Stanley, H E

    1995-05-01

    An open question in computational molecular biology is whether long-range correlations are present in both coding and noncoding DNA or only in the latter. To answer this question, we consider all 33301 coding and all 29453 noncoding eukaryotic sequences--each of length larger than 512 base pairs (bp)--in the present release of the GenBank to dtermine whether there is any statistically significant distinction in their long-range correlation properties. Standard fast Fourier transform (FFT) analysis indicates that coding sequences have practically no correlations in the range from 10 bp to 100 bp (spectral exponent beta=0.00 +/- 0.04, where the uncertainty is two standard deviations). In contrast, for noncoding sequences, the average value of the spectral exponent beta is positive (0.16 +/- 0.05) which unambiguously shows the presence of long-range correlations. We also separately analyze the 874 coding and the 1157 noncoding sequences that have more than 4096 bp and find a larger region of power-law behavior. We calculate the probability that these two data sets (coding and noncoding) were drawn from the same distribution and we find that it is less than 10(-10). We obtain independent confirmation of these findings using the method of detrended fluctuation analysis (DFA), which is designed to treat sequences with statistical heterogeneity, such as DNA's known mosaic structure ("patchiness") arising from the nonstationarity of nucleotide concentration. The near-perfect agreement between the two independent analysis methods, FFT and DFA, increases the confidence in the reliability of our conclusion. PMID:9963221

  13. Pseudocollinia brintoni gen. nov., sp. nov. (Apostomatida: Colliniidae), a parasitoid ciliate infecting the euphausiid Nyctiphanes simplex.

    PubMed

    Gmez-Gutirrez, J; Strder-Kypke, M C; Lynn, D H; Shaw, T C; Aguilar-Mndez, M J; Lpez-Corts, A; Martnez-Gmez, S; Robinson, C J

    2012-05-15

    A novel parasitoid ciliate, Pseudocollinia brintoni gen. nov., sp. nov. was discovered infecting the subtropical sac-spawning euphausiid Nyctiphanes simplex off both coasts of the Baja California peninsula, Mexico. We used microscopic, and genetic information to describe this species throughout most of its life cycle. Pseudocollinia is distinguished from other Colliniidae genera because it exclusively infects euphausiids, has a polymorphic life cycle, and has a small cone-shaped oral cavity whose left wall has a field of ciliated kinetosomes and whose opening is surrounded on the left and right by 2 'oral' kineties (or ciliary rows) that terminate at its anterior border. Two related species that infect different euphausiid species from higher latitudes in the northeastern Pacific Ocean, Collinia beringensis Capriulo and Small, 1986, briefly redescribed herein, and Collinia oregonensis Gmez-Gutirrez, Peterson, and Morado, 2006, are transferred to the genus Pseudocollinia. P. brintoni has between 12 and 18 somatic kineties, and its oral cavity has only 2 oral kineties, while P. beringensis comb. nov. has more somatic kineties, including 3 oral kineties. P. oregonensis comb. nov. has an intermediate number of somatic kineties. P. beringensis comb. nov. also infects Thysanoessa raschi (a new host species). SSU rRNA and cox1 gene sequences demonstrated that Pseudocollinia ciliates are apostome ciliates and that P. brintoni is different from P. beringensis comb. nov. High densities of rod-shaped bacteria (1.7 m length, 0.2 to 0.5 m diameter) were associated with P. brintoni. After euphausiid rupture, high concentrations of P. brintoni and bacteria cluster to form 3 to 6 cm long filaments where tomites encyst and transform to the phoront stage; this is a novel place for encystation. P. brintoni may complete its life cycle when the euphausiids feed on these filaments. PMID:22585303

  14. Association of Comorbidity Burden With Abnormal Cardiac Mechanics: Findings From the HyperGEN Study

    PubMed Central

    Selvaraj, Senthil; Aguilar, Frank G.; Martinez, Eva E.; Beussink, Lauren; Kim, Kwang?Youn A.; Peng, Jie; Rasmussen?Torvik, Laura; Sha, Jin; Irvin, Marguerite R.; Gu, C. Charles; Lewis, Cora E.; Hunt, Steven C.; Arnett, Donna K.; Shah, Sanjiv J.

    2014-01-01

    Background Comorbidities are common in heart failure (HF), and the number of comorbidities has been associated with poor outcomes in HF patients. However, little is known about the effect of multiple comorbidities on cardiac mechanics, which could impact the pathogenesis of HF. We sought to determine the relationship between comorbidity burden and adverse cardiac mechanics. Methods and Results We performed speckle?tracking analysis on echocardiograms from the HyperGEN study (n=2150). Global longitudinal, circumferential, and radial strain, and early diastolic (e') tissue velocities were measured. We evaluated the association between comorbidity number and cardiac mechanics using linear mixed effects models to account for relatedness among subjects. The mean age was 5114 years, 58% were female, and 47% were African American. Dyslipidemia and hypertension were the most common comorbidities (61% and 58%, respectively). After adjusting for left ventricular (LV) mass index, ejection fraction, and several potential confounders, the number of comorbidities remained associated with all indices of cardiac mechanics except global circumferential strain (eg, ?=?0.32 [95% CI ?0.44, ?0.20] per 1?unit increase in number of comorbidities for global longitudinal strain; ?=?0.16 [95% CI ?0.20, ?0.11] for e' velocity; P?0.0001 for both comparisons). Results were similar after excluding participants with abnormal LV geometry (P<0.05 for all comparisons). Conclusions Higher comorbidity burden is associated with worse cardiac mechanics, even in the presence of normal LV geometry. The deleterious effect of multiple comorbidities on cardiac mechanics may explain both the high comorbidity burden and adverse outcomes in patients who ultimately develop HF. PMID:24780206

  15. Natranaerobaculum magadiense gen. nov., sp. nov., an anaerobic, alkalithermophilic bacterium from soda lake sediment.

    PubMed

    Zavarzina, Daria G; Zhilina, Tatyana N; Kuznetsov, Boris B; Kolganova, Tatyana V; Osipov, Georgy A; Kotelev, Mikhail S; Zavarzin, Georgy A

    2013-12-01

    An obligately alkaliphilic, anaerobic, thermo- and halotolerant, spore-forming bacterium was isolated from sediments of soda lake Magadi (Kenya) and designated strain Z-1001(T). Cells of strain Z-1001(T) were straight, Gram-positive rods, slowly motile. Strain Z-1001(T) was found to be an obligate anaerobe. It grew within a pH range from 7.5 to 10.7 with an optimum at 9.25-9.5 (at 40 C), a temperature range from 20 to 57 C with an optimum at 45-50 C, and a NaCl concentration range from 0 to 1.55 M with an optimum at 1.2-1.4 M. Peptides, such as meat and yeast extracts, peptone and tryptone, were fermented by Z-1001(T). Carbohydrates did not support growth. With yeast extract as an electron donor, strain Z-1001(T) reduced S(2)O(3)(2-), NO(-)(3), AsO(3-)(4), Fe(III) citrate and anthraquinone-2,6-disulfonate (AQDS) as electron acceptors. The isolate was able to grow oligotrophically with a very small amount of yeast extract: 0.03 g l(-1). The main fatty acids were C16?:?0, C16?:?1?7c, C18?:?0 and C18?:?1?9. The DNA G+C content of the isolate was 35.6 mol%. 16S rRNA gene sequence analysis showed that strain Z-1001(T) is a member of family Natranaerobiaceae, clustering with the type strain of Natranaerobius thermophilus (95.8-96.0?% sequence similarity). On the basis of physiological and phylogenetic data it is proposed that strain Z-1001(T) (?=?DSM 24923(T)?=?VKM B-2666(T)) represents a novel genus and species, Natranaerobaculum magadiense gen. nov., sp. nov. PMID:23859946

  16. Methylomarinum vadi gen. nov., sp. nov., a methanotroph isolated from two distinct marine environments.

    PubMed

    Hirayama, Hisako; Fuse, Hiroyuki; Abe, Mariko; Miyazaki, Masayuki; Nakamura, Takamichi; Nunoura, Takuro; Furushima, Yasuo; Yamamoto, Hiroyuki; Takai, Ken

    2013-03-01

    Two aerobic methane-oxidizing bacterial strains were isolated from distinct marine environments in Japan. Strains IT-4(T) and T2-1 were Gram-stain-negative, aerobic, motile, plump short rods or oval-shaped bacteria with a single polar flagellum and type I intracytoplasmic membranes. They were obligate methanotrophs that grew only on methane or methanol. Each strain possessed the particulate methane monooxygenase (pMMO). The ribulose monophosphate pathway was operative for carbon assimilation. The strains grew best at 37 C, and did not grow at 45 C. NaCl was required for growth within a concentration range of 1-8?% (w/v). The major phospholipid fatty acids were C16?:?0, C16?:?1?7c, and C16?:?1?5t. The major isoprenoid quinone was MQ-8. The DNA G+C content was 50.9-51.7 mol%. The 16S rRNA gene sequences of the strains showed 99.4?% similarity to each other, and DNA-DNA hybridization analysis indicated that the strains were representatives of the same species. The 16S rRNA gene sequences were highly similar to some marine environmental sequences (94.0-97.7?% similarity), but did not show similarities more than 94?% with sequences of members of other related genera, such as Methylomicrobium, Methylobacter, Methylomonas and Methylosarcina. Phylogenies based on 16S rRNA gene sequences and deduced partial PmoA sequences, and the physiological and chemotaxonomic characteristics revealed that strains IT-4(T) and T2-1 represent a novel species of a new genus in the family Methylococcaceae, for which the name Methylomarinum vadi gen. nov., sp. nov. is proposed. The type strain is IT-4(T) (?=?JCM 13665(T)?=?DSM 18976(T)). PMID:22707534

  17. GenSeq: An updated nomenclature and ranking for genetic sequences from type and non-type sources

    PubMed Central

    Chakrabarty, Prosanta; Warren, Melanie; Page, Lawrence M.; Baldwin, Carole C.

    2013-01-01

    Abstract An improved and expanded nomenclature for genetic sequences is introduced that corresponds with a ranking of the reliability of the taxonomic identification of the source specimens. This nomenclature is an advancement of the Genetypes naming system, which some have been reluctant to adopt because of the use of the type suffix in the terminology. In the new nomenclature, genetic sequences are labeled genseq, followed by a reliability ranking (e.g., 1 if the sequence is from a primary type), followed by the name of the genes from which the sequences were derived (e.g., genseq-1 16S, COI). The numbered suffix provides an indication of the likely reliability of taxonomic identification of the voucher. Included in this ranking system, in descending order of taxonomic reliability, are the following: sequences from primary types genseq-1, secondary types genseq-2, collection-vouchered topotypes genseq-3, collection-vouchered non-types genseq-4, and non-types that lack specimen vouchers but have photo vouchers genseq-5. To demonstrate use of the new nomenclature, we review recently published new-species descriptions in the ichthyological literature that include DNA data and apply the GenSeq nomenclature to sequences referenced in those publications. We encourage authors to adopt the GenSeq nomenclature (note capital G and S when referring to the nomenclatural program) to provide a searchable tag (e.g., genseq; note lowercase g and s when referring to sequences) for genetic sequences from types and other vouchered specimens. Use of the new nomenclature and ranking system will improve integration of molecular phylogenetics and biological taxonomy and enhance the ability of researchers to assess the reliability of sequence data. We further encourage authors to update sequence information on databases such as GenBank whenever nomenclatural changes are made. PMID:24223486

  18. WallGen, Software to Construct Layered Cellulose-Hemicellulose Networks and Predict Their Small Deformation Mechanics1

    PubMed Central

    Kha, Hung; Tuble, Sigrid C.; Kalyanasundaram, Shankar; Williamson, Richard E.

    2010-01-01

    We understand few details about how the arrangement and interactions of cell wall polymers produce the mechanical properties of primary cell walls. Consequently, we cannot quantitatively assess if proposed wall structures are mechanically reasonable or assess the effectiveness of proposed mechanisms to change mechanical properties. As a step to remedying this, we developed WallGen, a Fortran program (available on request) building virtual cellulose-hemicellulose networks by stochastic self-assembly whose mechanical properties can be predicted by finite element analysis. The thousands of mechanical elements in the virtual wall are intended to have one-to-one spatial and mechanical correspondence with their real wall counterparts of cellulose microfibrils and hemicellulose chains. User-defined inputs set the properties of the two polymer types (elastic moduli, dimensions of microfibrils and hemicellulose chains, hemicellulose molecular weight) and their population properties (microfibril alignment and volume fraction, polymer weight percentages in the network). This allows exploration of the mechanical consequences of variations in nanostructure that might occur in vivo and provides estimates of how uncertainties regarding certain inputs will affect WallGen's mechanical predictions. We summarize WallGen's operation and the choice of values for user-defined inputs and show that predicted values for the elastic moduli of multinet walls subject to small displacements overlap measured values. Design of experiment methods provide systematic exploration of how changed input values affect mechanical properties and suggest that changing microfibril orientation and/or the number of hemicellulose cross-bridges could change wall mechanical anisotropy. PMID:20007450

  19. Surgical Treatment of Patients Enrolled in the National Registry of Genetically Triggered Thoracic Aortic Conditions (GenTAC)

    PubMed Central

    Song, Howard K.; Bavaria, Joseph E.; Kindem, Mark W.; Holmes, Kathryn W.; Milewicz, Dianna M.; Maslen, Cheryl L.; Pyeritz, Reed E.; Basson, Craig T.; Eagle, Kim; Tolunay, H. Eser; Kroner, Barbara L.; Dietz, Hal; Menashe, Victor; Devereux, Richard B.; Desvigne-Nickens, Patrice; Ravekes, William; Weinsaft, Jonathan W.; Brambilla, Donald; Stylianou, Mario P.; Hendershot, Tabitha; Mitchell, Megan S.; LeMaire, Scott A.

    2011-01-01

    Background Genetic disorders are an important cause of thoracic aortic aneurysms (TAAs) in young patients. Despite advances in the treatment of genetically triggered TAAs, the optimal syndrome-specific treatment approach remains undefined. We used data from the NIH-funded, multicenter National Registry of Genetically Triggered Thoracic Aortic Aneurysms and Cardiovascular Conditions (GenTAC) to characterize the contemporary surgical treatment of patients with genetically triggered TAAs. Methods GenTACs aim is to collect longitudinal clinical data and banked biospecimens from 2800 patients with genetically triggered TAAs. We analyzed data from all patients enrolled in GenTAC to date whose clinical data were available (n=606; mean age, 37.5 years). Results The patients primary diagnoses included Marfan syndrome (35.8%), bicuspid aortic valve with aneurysm (29.2%), and familial TAAs and dissections (10.7%). More than half of patients (56.4%) had undergone at least 1 operation; the most common indications were aneurysm (85.7%), valve dysfunction (65.8%), and dissection (25.4%). Surgical procedures included replacement of the aortic root (50.6%), ascending aorta (64.8%), aortic arch (27.9%), and descending or thoracoabdominal aorta (12.4%). Syndrome-specific differences in age, indications for surgery, and procedure type were identified. Conclusions Patients with genetically transmitted TAAs evaluated in tertiary care centers frequently undergo surgery. Aneurysm repairs most commonly involve the aortic root and ascending aorta; distal repairs are less common. Like TAAs themselves, complications of TAAs, including dissection and aortic valve dysfunction, are important indications for surgery. Future studies will focus on syndrome- and gene-specific phenotypes, biomarkers, treatments, and outcomes to improve the treatment of patients with TAAs. PMID:19699898

  20. Sumatrella chelonica gen. n., sp. n., a new remarkable genus and species from Indonesia, Sumatra (Acari, Uropodina, Oplitidae)

    PubMed Central

    Kontschn, Jen?

    2015-01-01

    Abstract A new genus Sumatrella gen. n. is described and illustrated based on the new species Sumatrella chelonica sp. n. collected in Sumatra, Indonesia. The new genus belongs to the family Oplitidae based on its hypertrichous internal malae and the absence of strongly sclerotized structures on the dorsal shield. The new genus is closely related to the genus Chelonuropoda Sellnick, 1954 but the transverse furrow on ventral idiosoma close to coxae IV and the strongly sclerotized C-shaped dorsal line are missing in the new genus. These characters can be found in species of Chelonuropoda. PMID:25829838

  1. Direct detection of Mycobacterium tuberculosis complex in nonrespiratory specimens by Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test.

    PubMed Central

    Gamboa, F; Manterola, J M; Viado, B; Matas, L; Gimnez, M; Lonca, J; Manzano, J R; Rodrigo, C; Cardona, P J; Padilla, E; Domnguez, J; Ausina, V

    1997-01-01

    The Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (AMTDT) was adapted for the detection of Mycobacterium tuberculosis complex in 224 nonrespiratory specimens from 188 patients. The sensitivity and specificity of the AMTDT for such specimens, after resolution of discrepant results, were 85.7 and 100%, respectively. Pretreatment of nonrespiratory specimens with sodium dodecyl (lauryl) sulfate is mandatory to obtain consistent and reproducible AMTDT results. The use of 500 microliters of decontaminated specimen improves the sensitivity of the test. Because the AMTDT detects stable rRNA from noncultivable bacilli, it is not useful for monitoring patients receiving treatment. PMID:8968935

  2. Characterization of some strains from human clinical sources which resemble "Leptotrichia sanguinegens": description of Sneathia sanguinegens sp. nov., gen. nov.

    PubMed

    Collins, M D; Hoyles, L; Tornqvist, E; von Essen, R; Falsen, E

    2001-11-01

    Three strains of a gram-negative, blood or serum requiring, rod-shaped bacterium recovered from human clinical specimens were characterised by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed the unknown rod-shaped strains are members of the same species as some fastidious isolates recovered from human blood specimens and previously designated "Leptotrichia sanguinegens". Based on phylogenetic and phenotypic evidence, it is proposed that the isolates from human sources be classified in a new genus Sneathia, as Sneathia sanguinegens gen. nov., sp. nov. The type strain of Sneathia sanguinegens is CCUG 41628T. PMID:11822670

  3. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform

    PubMed Central

    Chen, Rui; Im, Hogune; Snyder, Michael

    2015-01-01

    Multiple platforms are available for whole-exome enrichment and sequencing (WES). This protocol is based on the Roche NimbleGen SeqCap EZ Exome Library SR platform, which enriches for ~44 Mb of the human exonic regions. The SeqCap system uses 55- to 105-base DNA probes to capture known coding DNA sequences (CDS) from the NCBI Consensus CDS Database, RefSeq, and Sanger miRBase. The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer. PMID:25762419

  4. Degeneria halosauri (Bell 1887) gen. et comb. n. (Digenea: Gorgoderidae) from the deep-sea telost Halosauropsis macrochir.

    PubMed

    Campbell, R A

    1977-02-01

    The earliest reported trematode from a deep-sea fish, Distomum halosauri Bell 1887 collected by the H.M.S. Challenger expedition, is redescribed from fresh material taken from the type host in the northwest Atlantic. The species is assigned to Degeneria gen. et comb. n. Distinguishing characteristics are the combinaion of a pharynx, cirrus pouch with internal seminal vesicle, disposition of the uterus into the forebody, large eggs, and location in the excretory system of the host. The relationship of Degeneria to other gorgoderids is discussed. PMID:845742

  5. Notoatherix antiqua gen. et sp. nov., first fossil water snipe fly from the Late Jurassic of Australia (Diptera: Athericidae).

    PubMed

    Oberprieler, Stefanie K; Yeates, David K

    2014-01-01

    The first water snipe fly (Diptera: Tabanomorpha) fossil discovered in the Late Jurassic Talbragar Fish Bed in Australia is described and illustrated. Notoatherix antiqua gen. et sp. nov., described from a single wing specimen, is assigned to the family Athericidae based on the diagnostic feature of this family: the vein R2+3 ending very near to R1 (marginal cell closed). It is the first record of Athericidae from Australia and the oldest adult record of this family worldwide. PMID:25283652

  6. Osornodella gabrielae, n. gen. and n. sp., a new falklandellid (Amphipoda: Gammaridea) from freshwaters of the Chilean Coastal Range.

    PubMed

    Pérez-Schultheiss, Jorge

    2013-01-01

    The first species of falklandellid amphipod outside the Falkland Islands: Osornodella gabrielae n. gen., n. sp. is described from freshwaters of subterranean origin in the Coastal Range of Osorno province, Chile. The new taxon is characterized principally by the absence of secondary sexual characters in pereopods 3-4, uropod 3 aequiramous and telson slightly cleft. The new species is described and illustrated and its morphological relationships with other known species of this group are discussed. PMID:24613998

  7. A new member of troglobitic Carychiidae, Koreozospeum nodongense gen. et sp. n. (Gastropoda, Eupulmonata, Ellobioidea) is described from Korea

    PubMed Central

    Jochum, Adrienne; Prozorova, Larisa; Sharyi-ool, Mariana; Páll-Gergely, Barna

    2015-01-01

    Abstract A new genus of troglobitic Carychiidae Jeffreys, 1830 is designated from Nodong Cave, North Chungcheong Province, Danyang, South Korea. This remarkable find represents a great range extension and thus, a highly distant distribution of troglobitic Carychiidae in Asia. The Zospeum-like, carychiid snails were recently included, without a formal description, in records documenting Korean malacofauna. The present paper describes Koreozospeum Jochum & Prozorova, gen. n. and illustrates the type species, Koreozospeum nodongense Lee, Prozorova & Jochum, sp. n. using novel Nano-CT images, including a video, internal shell morphology, SEM and SEM-EDX elemental compositional analysis of the shell. PMID:26312456

  8. A new member of troglobitic Carychiidae, Koreozospeum nodongense gen. et sp. n. (Gastropoda, Eupulmonata, Ellobioidea) is described from Korea.

    PubMed

    Jochum, Adrienne; Prozorova, Larisa; Sharyi-Ool, Mariana; Pll-Gergely, Barna

    2015-01-01

    A new genus of troglobitic Carychiidae Jeffreys, 1830 is designated from Nodong Cave, North Chungcheong Province, Danyang, South Korea. This remarkable find represents a great range extension and thus, a highly distant distribution of troglobitic Carychiidae in Asia. The Zospeum-like, carychiid snails were recently included, without a formal description, in records documenting Korean malacofauna. The present paper describes Koreozospeum Jochum & Prozorova, gen. n. and illustrates the type species, Koreozospeum nodongense Lee, Prozorova & Jochum, sp. n. using novel Nano-CT images, including a video, internal shell morphology, SEM and SEM-EDX elemental compositional analysis of the shell. PMID:26312456

  9. Accuracy evaluation of ClimGen weather generator and daily to hourly disaggregation methods in tropical conditions

    NASA Astrophysics Data System (ADS)

    Safeeq, Mohammad; Fares, Ali

    2011-12-01

    Daily and sub-daily weather data are often required for hydrological and environmental modeling. Various weather generator programs have been used to generate synthetic climate data where observed climate data are limited. In this study, a weather data generator, ClimGen, was evaluated for generating information on daily precipitation, temperature, and wind speed at four tropical watersheds located in Hawai`i, USA. We also evaluated different daily to sub-daily weather data disaggregation methods for precipitation, air temperature, dew point temperature, and wind speed at Mākaha watershed. The hydrologic significance values of the different disaggregation methods were evaluated using Distributed Hydrology Soil Vegetation Model. MuDRain and diurnal method performed well over uniform distribution in disaggregating daily precipitation. However, the diurnal method is more consistent if accurate estimates of hourly precipitation intensities are desired. All of the air temperature disaggregation methods performed reasonably well, but goodness-of-fit statistics were slightly better for sine curve model with 2 h lag. Cosine model performed better than random model in disaggregating daily wind speed. The largest differences in annual water balance were related to wind speed followed by precipitation and dew point temperature. Simulated hourly streamflow, evapotranspiration, and groundwater recharge were less sensitive to the method of disaggregating daily air temperature. ClimGen performed well in generating the minimum and maximum temperature and wind speed. However, for precipitation, it clearly underestimated the number of extreme rainfall events with an intensity of >100 mm/day in all four locations. ClimGen was unable to replicate the distribution of observed precipitation at three locations (Honolulu, Kahului, and Hilo). ClimGen was able to reproduce the distributions of observed minimum temperature at Kahului and wind speed at Kahului and Hilo. Although the weather data generation and disaggregation methods were concentrated in a few Hawaiian watersheds, the results presented can be used to similar mountainous location settings, as well as any specific locations aimed at furthering the site-specific performance evaluation of these tested models.

  10. High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae

    PubMed Central

    2014-01-01

    The family Rickettsiaceae currently includes two genera: Orientia that contains one species, Orientiatsutsugamushi, and Rickettsia that contains 28 species. Occidentia massiliensis gen. nov., sp. nov. strain OS118T is the type strain of O. massiliensis gen. nov., sp. nov., the type species of the new genus Occidentia gen. nov. within the family Rickettsiaceae. This strain, whose genome is described here, was isolated in France from the soft tick Ornithodoros sonrai collected in Senegal. O. massiliensis is an aerobic, rod-shaped, Gram-negative, obligate intracellular bacillus that may be cultivated in BME/CTVM2 cells. Here we describe the features of O. massiliensis, together with the complete genomic sequencing and annotation. The 1,469,252 bp long genome (1 chromosome but no plasmid) contains 1,670 protein-coding and 41 RNA genes, including one rRNA operon. PMID:25780502

  11. Modeling and Evaluating Pilot Performance in NextGen: Review of and Recommendations Regarding Pilot Modeling Efforts, Architectures, and Validation Studies

    NASA Technical Reports Server (NTRS)

    Wickens, Christopher; Sebok, Angelia; Keller, John; Peters, Steve; Small, Ronald; Hutchins, Shaun; Algarin, Liana; Gore, Brian Francis; Hooey, Becky Lee; Foyle, David C.

    2013-01-01

    NextGen operations are associated with a variety of changes to the national airspace system (NAS) including changes to the allocation of roles and responsibilities among operators and automation, the use of new technologies and automation, additional information presented on the flight deck, and the entire concept of operations (ConOps). In the transition to NextGen airspace, aviation and air operations designers need to consider the implications of design or system changes on human performance and the potential for error. To ensure continued safety of the NAS, it will be necessary for researchers to evaluate design concepts and potential NextGen scenarios well before implementation. One approach for such evaluations is through human performance modeling. Human performance models (HPMs) provide effective tools for predicting and evaluating operator performance in systems. HPMs offer significant advantages over empirical, human-in-the-loop testing in that (1) they allow detailed analyses of systems that have not yet been built, (2) they offer great flexibility for extensive data collection, (3) they do not require experimental participants, and thus can offer cost and time savings. HPMs differ in their ability to predict performance and safety with NextGen procedures, equipment and ConOps. Models also vary in terms of how they approach human performance (e.g., some focus on cognitive processing, others focus on discrete tasks performed by a human, while others consider perceptual processes), and in terms of their associated validation efforts. The objectives of this research effort were to support the Federal Aviation Administration (FAA) in identifying HPMs that are appropriate for predicting pilot performance in NextGen operations, to provide guidance on how to evaluate the quality of different models, and to identify gaps in pilot performance modeling research, that could guide future research opportunities. This research effort is intended to help the FAA evaluate pilot modeling efforts and select the appropriate tools for future modeling efforts to predict pilot performance in NextGen operations.

  12. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

    PubMed Central

    2013-01-01

    Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified users query, advanced data searching based on the specified users query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search GenBank extends standard capabilities of the NCBI Entrez search engine in querying biomedical databases. The possibility of creating and saving macros in the search GenBank is a unique feature and has a great potential. The potential will further grow in the future with the increasing density of networks of relationships between data stored in particular databases. search GenBank is available for public use at http://sgb.biotools.pl/. PMID:23452691

  13. A new genus and species of isanthid sea anemone (Cnidaria: Anthozoa: Actiniaria) from Chilean Patagonia, Anthoparactis fossii n. gen. et sp

    NASA Astrophysics Data System (ADS)

    Hussermann, Verena; Rodrguez, Estefana

    2014-09-01

    We describe a new genus and species of sea anemone from Chilean Patagonia. Anthoparactis fossii n. gen. et sp. adds another acontiate genus and species to the family Isanthidae Carlgren, 1938. Anthoparactis n. gen. differs from the other isanthid genera in having the same number of mesenteries distally and proximally, acontia with basitrichs only, and a column with verrucae distally. Anthoparactis fossii n. sp. differs from the most similar species, Isoparactis fionae Lauretta et al., 2013, in the number of cycles of mesenteries and tentacles, structures of the column, colour pattern of the oral disc, cnidae, and geographical distribution. Isanthidae now includes seven genera and 11 species.

  14. The NextGen Model Atmosphere Grid. II. Spherically Symmetric Model Atmospheres for Giant Stars with Effective Temperatures between 3000 and 6800 K

    SciTech Connect

    Hauschildt, Peter H.; Allard, France; Ferguson, Jason; Baron, E.; Alexander, David R.

    1999-11-10

    We present the extension of our NextGen model atmosphere grid to the regime of giant stars. The input physics of the models presented here is nearly identical to that of the NextGen dwarf atmosphere models; however, spherical geometry is used self-consistently in the model calculations (including the radiative transfer). We revisit the discussion of the effects of spherical geometry on the structure of the atmospheres and the emitted spectra and discuss the results of non-LTE calculations for a few selected models. (c) 1999 The American Astronomical Society.

  15. Iranotrichia gen. n., a new genus of Scenopinidae (Diptera) from Iran, with a key to window fly genera of the world

    PubMed Central

    Winterton, Shaun L.; Gharali, Babak

    2011-01-01

    Abstract An unusual new genus of Scenopinidae, Iranotrichia gen. n., comprising two newly discovered species (Iranotrichia insolita sp. n. and Iranotrichia nigra sp. n.), is described from Iran. Iranotrichia gen. n. are scenopinine window flies with a habitus reminiscent of certain bee fly genera (Bombyliidae), based on colouration and elongate mouthparts and antennae. The phylogenetic placement of this distinctive new genus is discussed and a dichotomous key to world genera is presented. The genus name Kelseyana nom. n. is proposed to replace Caenoneura Krber, 1924, which was found to be preoccupied by Thomson (1870: 270) (Hymenoptera) and Kirby (1890: 136) (Odonata). PMID:22144855

  16. Comparative Evaluation of Two PCR-Based Methods for Detection of Methicillin-Resistant Staphylococcus aureus (MRSA): Xpert MRSA Gen 3 and BD-Max MRSA XT.

    PubMed

    Lepainteur, Margaux; Delattre, Sandrine; Cozza, Sophie; Lawrence, Christine; Roux, Anne-Laure; Rottman, Martin

    2015-06-01

    We compared two walk-away molecular diagnostic assays, the GeneXpert MRSA Gen 3 assay and the BD-Max MRSA XT assay. A total of 119 prospective swabs and 36 culture-positive samples were tested. Xpert MRSA Gen 3 had sensitivity of 95.7% and specificity of 100% versus 87.5% and 97.1% for BD-Max. The difference in agreement with the enriched culture results was significantly in favor of the Xpert assay (P < 0.02, McNemar nonparametric text). PMID:25878336

  17. Comparative Evaluation of Two PCR-Based Methods for Detection of Methicillin-Resistant Staphylococcus aureus (MRSA): Xpert MRSA Gen 3 and BD-Max MRSA XT

    PubMed Central

    Lepainteur, Margaux; Delattre, Sandrine; Cozza, Sophie; Lawrence, Christine; Roux, Anne-Laure

    2015-01-01

    We compared two walk-away molecular diagnostic assays, the GeneXpert MRSA Gen 3 assay and the BD-Max MRSA XT assay. A total of 119 prospective swabs and 36 culture-positive samples were tested. Xpert MRSA Gen 3 had sensitivity of 95.7% and specificity of 100% versus 87.5% and 97.1% for BD-Max. The difference in agreement with the enriched culture results was significantly in favor of the Xpert assay (P < 0.02, McNemar nonparametric text). PMID:25878336

  18. Paradevosia shaoguanensis gen. nov., sp. nov., isolated from a coking wastewater.

    PubMed

    Geng, Shuang; Pan, Xin-Chi; Mei, Ran; Wang, Ya-Nan; Sun, Ji-Quan; Liu, Xue-Ying; Tang, Yue-Qin; Wu, Xiao-Lei

    2015-01-01

    A Gram staining negative, rod-shaped, aerobic bacterial strain J5-3(T) with a single polar flagellum was isolated from coking wastewater collected from Shaoguan, Guangdong, China. It was motile and capable of optimal growth at pH 6-8, 30 °C, and 0-2 % (w/v) NaCl. Its predominant fatty acids were 11-methyl C18:1 ω7c (29.2 %), C16:0 (20.6 %), C19:0 cyclo ω8c (18.2 %), C18:0 (11.0 %), and C18:1 ω7c/C18:1 ω6c (10.9 %) when grown on trypticase soy agar. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids (GL1, GL2), and two unknown phospholipid (PL1, PL2). The predominant ubiquinone was Q-10, and the genome DNA G+C content was 61.7 mol %. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain J5-3(T) belonged to the family Hyphomicrobiaceae in Alphaproteobacteria. It shared the 16S rRNA gene sequence similarities of 93.8-96.1 % with the genus Devosia, 94.5-94.8 % with the genus Pelagibacterium, and <92.0 % with all the other type strains in family Hyphomicrobiaceae. It can be distinguished from the closest phylogenetic neighbors based on several phenotypic and genotypic features, including α-galactosidase activity, tetracycline susceptibility, major fatty acid composition, polar lipid profile, DNA gyrase B subunit (gyrB) gene sequence, and random-amplified polymorphic DNA profile. Therefore, we consider strain J5-3(T) to represent a novel species of a novel genus within the family Hyphomicrobiaceae, for which the name Paradevosia shaoguanensis gen. nov., sp. nov. is proposed. The type strain of Paradevosia shaoguanensis is J5-3(T) (=CGMCC 1.12430(T) =LMG 27409(T)). PMID:25234654

  19. Polymorphobacter multimanifer gen. nov., sp. nov., a polymorphic bacterium isolated from Antarctic white rock.

    PubMed

    Fukuda, Wakao; Chino, Yohzo; Araki, Shigeo; Kondo, Yuka; Imanaka, Hiroyuki; Kanai, Tamotsu; Atomi, Haruyuki; Imanaka, Tadayuki

    2014-06-01

    A Gram-stain-negative, non-spore-forming, aerobic, oligotrophic bacterium (strain 262-7(T)) was isolated from a crack of white rock collected in the Skallen region of Antarctica. Strain 262-7(T) grew at temperatures between -4 and 30 °C, with optimal growth at 25 °C. The pH range for growth was between pH 6.0 and 9.0, with optimal growth at approximately pH 7.0. The NaCl concentration range allowing growth was between 0.0 and 1.0%, with an optimum of 0.5%. Strain 262-7(T) showed an unprecedented range of morphological diversity in response to growth conditions. Cells grown in liquid medium were circular or ovoid with smooth surfaces in the lag phase. In the exponential phase, ovoid cells with short projections were observed. Cells in the stationary phase possessed long tentacle-like projections intertwined intricately. By contrast, cells grown on agar plate medium or in liquid media containing organic compounds at low concentration exhibited short- and long-rod-shaped morphology. These projections and morphological variations clearly differ from those of previously described bacteria. Ubiquinone 10 was the major respiratory quinone. The major fatty acids were C(17 : 1)ω6c (28.2%), C(16 : 1)ω7c (22.6%), C(18 : 1)ω7c (12.9%) and C(15 : 0) 2-OH (12.3%). The G+C content of genomic DNA was 68.0 mol%. Carotenoids were detected from the cells. Comparative analyses of 16S rRNA gene sequences indicated that strain 262-7(T) belongs to the family Sphingomonadaceae, and that 262-7(T) should be distinguished from known genera in the family Sphingomonadaceae. According to the phylogenetic position, physiological characteristics and unique morphology variations, strain 262-7(T) should be classified as a representative of a novel genus of the family Sphingomonadaceae. Here, a novel genus and species with the name Polymorphobacter multimanifer gen. nov., sp. nov. is proposed (type strain 262-7(T) = JCM 18140(T) = ATCC BAA-2413(T)). The novel species was named after its morphological diversity and formation of unique projections. PMID:24651306

  20. Rosenbergiella nectarea gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from floral nectar.

    PubMed

    Halpern, Malka; Fridman, Svetlana; Atamna-Ismaeel, Nof; Izhaki, Ido

    2013-11-01

    Gram-negative, rod-shaped, oxidase-negative, facultatively anaerobic, yellow-orange-pigmented and motile bacterial strains, designated 8N4(T), 9N2 and 10N3, were isolated from flower nectar of Amygdalus communis (almond) and Citrus paradisi (grapefruit). The 16S rRNA gene sequences of the strains shared highest sequence similarity of 97.0 % with that of Phaseolibacter flectens ATCC 12775(T) and lower similarity with sequences from other type strains of genera of the Enterobacteriaceae. A polyphasic approach that included determination of phenotypic properties and phylogenetic analysis based on 16S rRNA, gyrB, rpoB and atpD gene sequences supported the classification of strains 8N4(T), 9N2 and 10N3 within a novel species in a novel genus in the family Enterobacteriaceae. Strain 8N4(T), and the reference strains of the novel species, grew at 4-35 °C (optimum, 28-30 °C), with 0-5.0 % NaCl (optimum, 3 % NaCl) and with 0-60 % sucrose (optimum, 10-25 % sucrose). Their major cellular fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain 8N4(T) was 46.8 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the floral nectar isolates are classified within a novel species in a new genus in the family Enterobacteriaceae, for which the name Rosenbergiella nectarea gen. nov., sp. nov. is proposed. The type strain of Rosenbergiella nectarea is 8N4(T) ( = LMG 26121(T) = DSM 24150(T)). PMID:23832968

  1. Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome

    PubMed Central

    Schmidt, Johanna; Taipale, Sami J.; Doolittle, W. Ford; Koll, Ulrike

    2014-01-01

    A pure culture of an actinobacterium previously described as ‘Candidatus Rhodoluna lacicola’ strain MWH-Ta8 was established and deposited in two public culture collections. Strain MWH-Ta8T represents a free-living planktonic freshwater bacterium obtained from hypertrophic Meiliang Bay, Lake Taihu, PR China. The strain was characterized by phylogenetic and taxonomic investigations, as well as by determination of its complete genome sequence. Strain MWH-Ta8T is noticeable due to its unusually low values of cell size (0.05 µm3), genome size (1.43 Mbp), and DNA G+C content (51.5 mol%). Phylogenetic analyses based on 16S rRNA gene and RpoB sequences suggested that strain MWH-Ta8T is affiliated with the family Microbacteriaceae with Pontimonas salivibrio being its closest relative among the currently described species within this family. Strain MWH-Ta8T and the type strain of Pontimonas salivibrio shared a 16S rRNA gene sequence similarity of 94.3 %. The cell-wall peptidoglycan of strain MWH-Ta8T was of type B2β (B10), containing 2,4-diaminobutyric acid as the diamino acid. The predominant cellular fatty acids were anteiso-C15 : 0 (36.5 %), iso-C16 : 0 (16.5 %), iso-C15 : 0 (15.6 %) and iso-C14 : 0 (8.9 %), and the major (>10 %) menaquinones were MK-11 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and two unknown glycolipids. The combined phylogenetic, phenotypic and chemotaxonomic data clearly suggest that strain MWH-Ta8T represents a novel species of a new genus in the family Microbacteriaceae, for which the name Rhodoluna lacicola gen. nov., sp. nov. is proposed. The type strain of the type species is MWH-Ta8T ( = DSM 23834T = LMG 26932T). PMID:24984700

  2. Tonsilliphilus suis gen. nov., sp. nov., causing tonsil infections in pigs.

    PubMed

    Azuma, Ryozo; Ung-Bok, Bak; Murakami, Satoshi; Ishiwata, Hiroyuki; Osaki, Makoto; Shimada, Nobuaki; Ito, Yasuichiro; Miyagawa, Eichi; Makino, Takashi; Kudo, Takuji; Takahashi, Yoko; Yano, Ikuya; Murata, Ryo; Yokoyama, Eiji

    2013-07-01

    A micro-organism resembling members of the genus Dermatophilus, strain W254(T), which was isolated from the submandibular lymph node of a pig, and an additional 16 strains isolated from swine tonsils, were studied to establish their taxonomic status. Although all 17 strains were isolated anaerobically under an atmosphere of 100 % CO2, all of them were aerotolerant anaerobes. The micro-organisms showed at least five cellular morphologies: (i) a radially protrusive thallus, which proliferated into tuber-like cells; (ii) segmentation in both tubers and thallus followed by multilocule formation, (iii) development of coccoid forms in the locules; (iv) a change from the coccoid forms to zoospores; (v) resting cells, which were able to develop into protrusive thalli again. The micro-organisms were positive for nitrate reduction, but negative for catalase, indole production, hydrolysis of urea and gelatin liquefaction. Milk was not decomposed and none of the strains was haemolytic. A total of 16 compounds, including glucose, were utilized as sole carbon sources and seven compounds, including l-arabinose, were not utilized. Three out of the 17 strains were subjected to further studies. The micro-organisms had meso-diaminopimelic acid in their peptidoglycan and galactose, glucose, madurose and a trace of mannose in their whole-cell sugar patterns. The major phospholipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol.Cellular fatty acids were C15 : 0 (35.7-23.1 %), C16 : 0 (5.9-2.4 %) C17 : 0 (62.9-39.5 %), C17 : 1 (24.4-0 %) and C18 : 0 (3-1.6 %). The predominant menaquinone was MK-8 (H4). The G+C content of the DNA was 69.6-71.8 mol%. Analysis of the 16S rRNA gene sequences showed that the strains clustered with the type strains of members of the family Dermatophilaceae. Based on the polyphasic taxonomic characterization carried out, all 17 strains are considered to belong to a novel species in a new genus, for which the name Tonsilliphilus suis gen. nov., sp. nov. is proposed. The type strain of the type species is W254(T) ( = ATCC 35846(T) = CCM 3774(T) = DSM 21880(T) = JCM 15727(T)). PMID:23243095

  3. Telmatocola sphagniphila gen. nov., sp. nov., a Novel Dendriform Planctomycete from Northern Wetlands

    PubMed Central

    Kulichevskaya, Irina S.; Serkebaeva, Yulia M.; Kim, Yongkyu; Rijpstra, W. Irene C.; Damst, Jaap S. Sinninghe; Liesack, Werner; Dedysh, Svetlana N.

    2012-01-01

    Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2T (=DSM 23888T?=?VKM B-2710T), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.07.0 (optimum pH 5.05.5) and at 630C (optimum 2026C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (?0.025%). In contrast to other described planctomycetes, strains SP2T and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1?5c, C18:1?5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (910 double bonds) and C30:1/C32:1 (?-1) hydroxy fatty acids. The G?+?C content of the DNA is 58.559.0?mol%. Strains SP2T and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov. PMID:22529844

  4. Clostridiisalibacter paucivorans gen. nov., sp. nov., a novel moderately halophilic bacterium isolated from olive mill wastewater.

    PubMed

    Liebgott, Pierre-Pol; Joseph, Manon; Fardeau, Marie-Laure; Cayol, Jean-Luc; Falsen, Enevold; Chamkh, Fatima; Qatibi, Abdel-Illah; Labat, Marc

    2008-01-01

    A moderately halophilic, strictly anaerobic bacterium, designated 37HS60(T), was isolated from an olive mill wastewater in southern Morocco (Marrakesh). The cells were straight, motile and stained Gram-positive, forming spherical and terminal spores and with an atypical thick and stratified multilayered cell wall. Major fatty acid components were iso-C17:1omega10c or anteiso-C17:1omega3c (19.3%), C14:0 (14.3%), C16:1omega7c (9.9%), C16:1omega7c DMA (8.5%) and C16:0 (7.6%). Strain 37HS60(T) grew from 20 to 50 degrees C with an optimum at 40-45 degrees C, and growth was observed from pH 5.5 to 8.5 with an optimum of 6.8. The salinity range for growth was 10-100 g NaCl l(-1) with an optimum at 50 g NaCl l(-1). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 37HS60(T) fell within the evolutionary radiation enclosed by cluster XII of the Clostridium subphylum. Strain 37HS60(T) exhibited highest 16S rRNA gene sequence similarity of 92.0% with Caloranaerobacter azorensis and 90.6% with Clostridium purinilyticum. Moreover, 37HS60(T) did not grow on basal medium with hexose or pentose sugars as carbon and energy sources. Pyruvate, fumarate and succinate were the best substrates for 37HS60(T) growth with 1.0 g yeast extract l(-1). The DNA G+C content was 33.0 mol%. Due to its phenotypic and genotypic characteristics, isolate 37HS60(T) is proposed as a novel species of a new genus, Clostridiisalibacter paucivorans gen. nov., sp. nov. The type strain is 37HS60(T) (=JCM 14354(T)=CCUG 53849(T)). PMID:18175684

  5. Oceanibulbus indolifex gen. nov., sp. nov., a North Sea alphaproteobacterium that produces bioactive metabolites.

    PubMed

    Wagner-Döbler, Irene; Rheims, Holger; Felske, Andreas; El-Ghezal, Aymen; Flade-Schröder, Dirk; Laatsch, Hartmut; Lang, Siegmund; Pukall, Rüdiger; Tindall, Brian J

    2004-07-01

    A water sample from the North Sea was used to isolate the abundant heterotrophic bacteria that are able to grow on complex marine media. Isolation was by serial dilution and spread plating. Phylogenetic analysis of nearly complete 16S rRNA gene sequences revealed that one of the strains, HEL-45T, had 97.4% sequence similarity to Sulfitobacter mediterraneus and 96.5 % sequence similarity to Staleya guttiformis. Strain HEL-45T is a Gram-negative, non-motile rod and obligate aerobe and requires sodium and 1-7% sea salts for growth. It contains storage granules and does not produce bacteriochlorophyll. Optimal growth temperatures are 25-30 degrees C. The DNA base composition (G+C content) is 60.1 mol%. Strain HEL-45T has Q10 as the dominant respiratory quinone. The major polar lipids are phosphatidyl glycerol, diphosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine and an aminolipid. The fatty acids comprise 18 : 1omega7c, 18 : 0, 16 : 1omega7c, 16 : 0, 3-OH 10 : 0, 3-OH 12 : 1 (or 3-oxo 12 : 0) and traces of an 18 : 2 fatty acid. Among the hydroxylated fatty acids only 3-OH 12 : 1 (or 3-oxo 12 : 0) appears to be amide linked, whereas 3-OH 10 : 0 appears to be ester linked. The minor fatty acid components (between 1 and 7%) allow three subgroups to be distinguished in the Sulfitobacter/Staleya clade, placing HEL-45T into a separate lineage characterized by the presence of 3-OH 12 : 1 (or 3-oxo 12 : 0) and both ester- and amide-linked 16 : 1omega7c phospholipids. HEL-45T produces indole and derivatives thereof, several cyclic dipeptides and thryptanthrin. Phylogenetic analysis of 16S rRNA gene sequences and chemotaxonomic data support the description of a new genus and species, to include Oceanibulbus indolifex gen. nov., sp. nov., with the type strain HEL-45T (=DSM 14862T=NCIMB 13983T). PMID:15280288

  6. Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters.

    PubMed

    Ogg, Christopher D; Patel, Bharat K C

    2010-06-01

    A strictly anaerobic, thermophilic bacterium, designated strain AeB(T), was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeB(T) were slightly curved rods (2.5-6.0x1.0 mum) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone-yeast extract-Casamino acids medium at 50 degrees C (range 37-55 degrees C) and pH 7 (range pH 5-9). Strain AeB(T) grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeB(T) increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4+/-1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeB(T) is a member of the family Clostridiaceae, class Clostridia, phylum 'Firmicutes', and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8-90.9 %). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain AeB(T) is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeB(T) (=JCM 15555(T)=KCTC 5667(T)). PMID:19671710

  7. The Photosynthetic Apparatus and Its Regulation in the Aerobic Gammaproteobacterium Congregibacter litoralis gen. nov., sp. nov

    PubMed Central

    Spring, Stefan; Lünsdorf, Heinrich; Fuchs, Bernhard M.; Tindall, Brian J.

    2009-01-01

    Background There is accumulating evidence that in some marine environments aerobic bacteriochlorophyll a-producing bacteria represent a significant part of the microbial population. The interaction of photosynthesis and carbon metabolism in these interesting bacteria is still largely unknown and requires further investigation in order to estimate their contribution to the marine carbon cycle. Methodology/Principal Findings Here, we analyzed the structure, composition and regulation of the photosynthetic apparatus in the obligately aerobic marine gammaproteobacterium KT71T. Photoheterotrophically grown cells were characterized by a poorly developed lamellar intracytoplasmic membrane system, a type 1 light-harvesting antenna complex and a photosynthetic reaction center associated with a tetraheme cytochrome c. The only photosynthetic pigments produced were bacteriochlorophyll a and spirilloxanthin. Under semiaerobic conditions KT71T cells expressing a photosynthetic apparatus showed a light-dependent increase of growth yield in the range of 1.3–2.5 fold. The expression level of the photosynthetic apparatus depended largely on the utilized substrate, the intermediary carbon metabolism and oxygen tension. In addition, pigment synthesis was strongly influenced by light, with blue light exerting the most significant effect, implicating that proteins containing a BLUF domain may be involved in regulation of the photosynthetic apparatus. Several phenotypic traits in KT71T could be identified that correlated with the assumed redox state of growing cells and thus could be used to monitor the cellular redox state under various incubation conditions. Conclusions/Significance In a hypothetical model that explains the regulation of the photosynthetic apparatus in strain KT71T we propose that the expression of photosynthesis genes depends on the cellular redox state and is maximal under conditions that allow a balanced membrane redox state. So far, bacteria capable of an obligately aerobic, photosynthetic metabolism constitute a unique phenotype within the class Gammaproteobacteria, so that it is justified to propose a new genus and species, Congregibacter litoralis gen. nov, sp. nov., represented by the type strain KT71T ( = DSM 17192T = NBRC 104960T). PMID:19287491

  8. Phycicola gilvus gen. nov., sp. nov., an actinobacterium isolated from living seaweed.

    PubMed

    Lee, Dong Wan; Lee, Jin Mi; Seo, Jae Pyo; Schumann, Peter; Kim, Sae Jae; Lee, Soon Dong

    2008-06-01

    A Gram-positive, aerobic, non-mycelium-forming actinomycete, designated strain SSWW-21(T), was isolated from a living seaweed sample on the coast of Jeju, Republic of Korea. Cells of the organism were rod-shaped or coccoid depending on culture age. Short rods were observed in young cultures, whereas older cultures predominantly consisted of coccoid cells. Rod-shaped cells were motile by means of flagella, but coccoid cells were non-motile. Budding-like cell division was observed. The temperature and pH for growth were 4-30 degrees C and pH 6.1-10.1. Growth occurred in the presence of up to 2 % NaCl. Phylogenetic analyses showed that the organism formed a distinct clade within the family Microbacteriaceae. Comparative 16S rRNA gene sequence analyses showed that strain SSWW-21(T) was related most closely to the type strains of Okibacterium fritillariae (96.8 % similarity), Leifsonia poae (96.8 %) and Agreia bicolorata (96.6 %). Levels of 16S rRNA gene sequence similarity between the new isolate and members of other genera within the family Microbacteriaceae were in the range 93.1-96.3 %. The cell-wall peptidoglycan of strain SSWW-21(T) was of the B-type (2,4-diaminobutyric acid as the diagnostic diamino acid). The acyl type of the muramic acid was acetyl. The predominant menaquinone was MK-11. The polar lipid profile contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were not present. The major cellular fatty acids were saturated branched-chain components (anteiso-C(15 : 0) and anteiso-C(17 : 0)). The G+C content of the DNA was 69.8 mol%. On the basis of the phenotypic and phylogenetic data presented, strain SSWW-21(T) is considered to represent a novel species of a new genus within the family Microbacteriaceae, for which the name Phycicola gilvus gen. nov., sp. nov. is proposed. The type strain of Phycicola gilvus is SSWW-21(T) (=KCTC 19185(T) =DSM 18319(T)). PMID:18523172

  9. Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop.

    PubMed

    Li, Leilei; Praet, Jessy; Borremans, Wim; Nunes, Olga C; Manaia, Célia M; Cleenwerck, Ilse; Meeus, Ivan; Smagghe, Guy; De Vuyst, Luc; Vandamme, Peter

    2015-01-01

    In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as 'Commensalibacter intestini', except for two isolates (R-52486 and LMG 28161(T)) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161(T) was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877(T) (96.5%), which corresponded with genus level divergence in the family Acetobacteraceae. Isolate LMG 28161(T) was subjected to whole-genome shotgun sequencing; a 16S-23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae. The DNA G+C content of strain LMG 28161(T) was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161(T) were similar to those of established AAB species [with C18:1ω7c (43.1%) as the major component], but the amounts of fatty acids such as C19:0 cyclo ω8c, C14:0 and C14:0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161(T) ( =DSM 28636(T) =R-52487(T)) as the type strain of the type species. PMID:25336723

  10. Ammoniibacillus agariperforans gen. nov., sp. nov., a thermophilic, agar-degrading bacterium isolated from compost.

    PubMed

    Sakai, Masao; Deguchi, Daigo; Hosoda, Akifumi; Kawauchi, Tomohiro; Ikenaga, Makoto

    2015-02-01

    A thermophilic, agar-degrading bacterium, strain FAB2(T), was isolated from sewage sludge compost. According to phylogenetic analysis based on 16S rRNA gene sequences, strain FAB2(T) belonged to the family Paenibacillaceae within the phylum Firmicutes. However, FAB2(T) was different enough at the genus level from closely related species. The percentages of 16S rRNA gene sequence similarity with related organisms were 90.4 % for Thermobacillus xylanilyticus, 91.8 % for Paenibacillus barengoltzii, 89.4 % for Cohnella lupini, 90.1 % for Fontibacillus aquaticus, and 89.0 % for Saccharibacillus sacchari. Morphological and physiological analyses revealed that the strain was motile, rod-shaped, Gram-stain-positive, aerobic and able to form oval endospores in swollen sporangia. Ammonium was required as a nitrogen source while nitrate, nitrite, urea and glutamate were not utilized. Catalase and oxidase activities were weakly positive and positive, respectively. The bacterium grew in the temperature range of 50-65 C and in media with pH 7.5 to 9.0. Optimal growth occurred at 60 C and pH 8.0-8.6. Growth was inhibited at pH?7.0 and NaCl concentrations ?2.5 % (w/v). In chemotaxonomic characterization, MK-7 was identified as the dominant menaquinone. Major fatty acids were iso-C16 : 0 and C16 : 0. Dominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phosphatidylcholine was present in a moderate amount. The diamino acid in the cell wall was meso-diaminopimelic acid. The G+C content of the genomic DNA was 49.5 mol% in a nucleic acid study. On the basis of genetic and phenotypic characteristics, strain FAB2(T) (?= NBRC 109510(T)?= KCTC 33130(T)) showed characteristics suitable for classification as the type strain of a novel species of a new genus in the family Paenibacillaceae, for which the name Ammoniibacillus agariperforans gen. nov., sp. nov. is proposed. PMID:25404482

  11. Should we resurface the patella in total knee replacement? Experience with the Nex Gen prothesis.

    PubMed

    Tabutin, J; Banon, F; Catonne, Y; Grobost, J; Tessier, J L; Tillie, B

    2005-10-01

    Patellar resurfacing is a controversial issue in primary total knee replacement. So, we took advantage of a large study to try and answer this question. An open prospective multicentric study was conducted about the outcome of the Nex Gen Total Knee prosthesis with clinical and radiological follow-up at regular intervals (1, 2 and 5 years). The data were centrally collected and analyzed by independent observers. A total of whole 5,915 cases were included (487 in the French group); incidences of patello-femoral pain were observed in both French and international groups and compared between cases with or without resurfaced patellae. Only osteoarthritic cases were selected for this particular study. Statistical analysis was performed using a Pearson's Chi-square test with a 95% confidence interval. The frequency of preoperative pain was significantly higher in the French group; 85.1% versus 66.6% (p<0.05). No patello-femoral pain appeared in preoperatively painless patients in the French group. The frequency of lateral patellar release was similar in both groups. 35.7% of the patellae were resurfaced in the international group versus 98.8% in the French one. At 2 years, patello-femoral pain was observed in 6.3% of cases in the former group versus 0.7% in the latter one. The risk of having patello-femoral pain was 9.45 times higher in the international group. When considering resurfaced cases in both groups the risk of having anterior knee pain was not significantly different (p=0.35). In the French group, one case out of nine (11.1%) with patello-femoral pain had not been resurfaced, while 129 cases out of 151 (85.4%) had not had a resurfacing in the international group. This emphasizes the effect of patellar implant on pain. Although patello-femoral pain is multifactorial, this analysis tool is powerful in getting rid of the "center effect " (cf Swedish register). Even if a longer follow-up for confirmation is needed, our data favor patellar resurfacing with this type of implant in spite of the fact that the trochlear design was considered as anatomical. PMID:15800755

  12. Fuchsiella alkaliacetigena gen. nov., sp. nov., an alkaliphilic, lithoautotrophic homoacetogen from a soda lake.

    PubMed

    Zhilina, Tatyana N; Zavarzina, Daria G; Panteleeva, Angela N; Osipov, Georgy A; Kostrikina, Nadezhda A; Tourova, Tatyana P; Zavarzin, Georgy A

    2012-07-01

    The first alkaliphilic obligately anaerobic hydrogenotrophic homoacetogenic bacterium, strain Z-7100(T), was isolated from sediments of the soda-depositing soda lake Tanatar III (Altay, Russia). Cells were thin, flexible rods, motile, Gram-negative and spore-forming. The organism was an obligate alkaliphile, growing at pH 8.5 to 10.5, with optimum growth at pH 8.8-9.3, and it grew in soda brines containing 1.9-4.7 M total Na(+) (optimum at 2.8-3.3 M). It exhibited an obligate dependence upon sodium carbonate but not upon chloride ions with an NaCl range for growth of 0-14% (w/v) and an optimum at 7.0-8.5% (w/v). The isolate was mesophilic and grew at temperatures from 25 to 45 C, with an optimum at 40 C. An H(2)+CO(2) mixture, ethanol, pyruvate and lactate were utilized with the formation of acetate as the sole metabolic product. Carbohydrates and amino acids did not support growth. The isolate had a respiratory type of metabolism, reducing NO3(-), SeO(4)(2-) or anthraquinone-2,6-disulfonate (as electron acceptors with ethanol as an electron donor). It was able to grow chemolithotrophically on H(2)+CO(2) in medium supplemented with a vitamin solution only. The major cellular fatty acids were the saturated fatty acids anteiso-C(15), C(14:0) and C(16:0) and the aldehydes C(16), C(14) and anteiso-C(15). The DNA G+C content of the isolate was 32.0 mol%. 16S rRNA gene sequence analysis showed that strain Z-7100(T) is a member of the order Halanaerobiales and represents a new branch within the family Halobacteroidaceae, clustering with the type strain of Selenihalanaerobacter shriftii (92.9% gene sequence similarity). On the basis of its physiological characteristics and phylogenetic position, the isolate is considered to represent a novel species in a new genus within the family Halobacteroidaceae. The name Fuchsiella alkaliacetigena gen. nov., sp. nov. is proposed. The type strain of the type species is Z-7100(T) (=DSM 24880(T)=VKM B-2667(T)). PMID:21908678

  13. Desmozoon lepeophtherii n. gen., n. sp., (Microsporidia: Enterocytozoonidae) infecting the salmon louse Lepeophtheirus salmonis (Copepoda: Caligidae)

    PubMed Central

    2009-01-01

    Background A microsporidian was previously reported to infect the crustacean parasite, Lepeophtheirus salmonis (Krøyer, 1837) (Copepoda, Caligidae), on farmed Atlantic salmon (Salmo salar L.) in Scotland. The microsporidian was shown to be a novel species with a molecular phylogenetic relationship to Nucleospora (Enterocytozoonidae), but the original report did not assign it to a genus or species. Further studies examined the development of the microsporidian in L. salmonis using electron microscopy and re-evaluated the molecular findings using new sequence data available for the group. Here we report a full description for the microsporidian and assign it to a new genus and species. Results The microsporidian infects subcuticular cells that lie on the innermost region of the epidermal tissue layer beneath the cuticle and along the internal haemocoelic divisions. The mature spores are sub-spherical with a single nucleus and an isofilar polar filament with 5-8 turns in a double coil. The entire development is in direct contact with the host cell cytoplasm and is polysporous. During early merogony, a diplokaryotic nuclear arrangement exists which is absent throughout the rest of the developmental cycle. Large merogonial plasmodia form which divide to form single uninucleate sporonts. Sporogonial plasmodia were not observed; instead, binucleate sporonts divide to form two sporoblasts. Prior to final division, there is a precocious development of the polar filament extrusion apparatus which is associated with large electron lucent inclusions (ELIs). Analyses of DNA sequences reveal that the microsporidian is robustly supported in a clade with other members of the Enterocytozoonidae and confirms a close phylogenetic relationship with Nucleospora. Conclusion The ultrastructural findings of the precocious development of the polar filament and the presence of ELIs are consistent with those of the Enterocytozoonidae. However, the confirmed presence of an early diplokaryotic stage and a merogonial plasmodium that divides to yield uninucleate sporonts instead of transforming into a sporogonial syncitium, are features not currently associated with the family. Yet, analyses of DNA sequence data clearly place the microsporidian within the Enterocytozoonidae. Therefore, due to the novelty of the copepod host, the ultrastructural findings and the robust nature of the phylogenetic analyses, a new genus should be created within the Enterocytozoonide; Desmozoon lepeophtherii n. gen. n. sp. is proposed. PMID:19943930

  14. A graph based algorithm for adaptable dynamic airspace configuration for NextGen

    NASA Astrophysics Data System (ADS)

    Savai, Mehernaz P.

    The National Airspace System (NAS) is a complicated large-scale aviation network, consisting of many static sectors wherein each sector is controlled by one or more controllers. The main purpose of the NAS is to enable safe and prompt air travel in the U.S. However, such static configuration of sectors will not be able to handle the continued growth of air travel which is projected to be more than double the current traffic by 2025. Under the initiative of the Next Generation of Air Transportation system (NextGen), the main objective of Adaptable Dynamic Airspace Configuration (ADAC) is that the sectors should change to the changing traffic so as to reduce the controller workload variance with time while increasing the throughput. Change in the resectorization should be such that there is a minimal increase in exchange of air traffic among controllers. The benefit of a new design (improvement in workload balance, etc.) should sufficiently exceed the transition cost, in order to deserve a change. This leads to the analysis of the concept of transition workload which is the cost associated with a transition from one sectorization to another. Given two airspace configurations, a transition workload metric which considers the air traffic as well as the geometry of the airspace is proposed. A solution to reduce this transition workload is also discussed. The algorithm is specifically designed to be implemented for the Dynamic Airspace Configuration (DAC) Algorithm. A graph model which accurately represents the air route structure and air traffic in the NAS is used to formulate the airspace configuration problem. In addition, a multilevel graph partitioning algorithm is developed for Dynamic Airspace Configuration which partitions the graph model of airspace with given user defined constraints and hence provides the user more flexibility and control over various partitions. In terms of air traffic management, vertices represent airports and waypoints. Some of the major (busy) airports need to be given more importance and hence treated separately. Thus the algorithm takes into account the air route structure while finding a balance between sector workloads. The performance of the proposed algorithms and performance metrics is validated with the Enhanced Traffic Management System (ETMS) air traffic data.

  15. Telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands.

    PubMed

    Kulichevskaya, Irina S; Serkebaeva, Yulia M; Kim, Yongkyu; Rijpstra, W Irene C; Damst, Jaap S Sinninghe; Liesack, Werner; Dedysh, Svetlana N

    2012-01-01

    Members of the phylum Planctomycetes are common inhabitants of northern wetlands. We used barcoded pyrosequencing to survey bacterial diversity in an acidic (pH 4.0) Sphagnum peat sampled from the peat bog Obukhovskoye, European North Russia. A total of 21189 bacterial 16S rRNA gene sequences were obtained, of which 1081 reads (5.1%) belonged to the Planctomycetes. Two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been available. Here, we describe two organisms from one of these previously uncultivated planctomycete groups. One isolate, strain OB3, was obtained from the peat sample used in our molecular study, while another strain, SP2(T) (=DSM 23888(T)?=?VKM B-2710(T)), was isolated from the peat bog Staroselsky moss. Both isolates are represented by aerobic, budding, pink-pigmented, non-motile, spherical cells that are arranged in unusual, dendriform-like structures during growth on solid media. These bacteria are moderately acidophilic and mesophilic, capable of growth at pH 4.0-7.0 (optimum pH 5.0-5.5) and at 6-30C (optimum 20-26C). The preferred growth substrates are various heteropolysaccharides and sugars, the latter being utilized only if provided in low concentrations (?0.025%). In contrast to other described planctomycetes, strains SP2(T) and OB3 possess weak cellulolytic potential. The major fatty acids are C16:1?5c, C18:1?5c, C16:0, and C18:0. Characteristic lipids are the n-C31 polyunsaturated alkene (9-10 double bonds) and C30:1/C32:1 (?-1) hydroxy fatty acids. The G?+?C content of the DNA is 58.5-59.0?mol%. Strains SP2(T) and OB3 share identical 16S rRNA gene sequences, which exhibit only 86 and 87% similarity to those of Gemmata obscuriglobus and Zavarzinella formosa. Based on the characteristics reported here, we propose to classify these novel planctomycetes as representatives of a novel genus and species, Telmatocola sphagniphila gen. nov., sp. nov. PMID:22529844

  16. Methyloparacoccus murrellii gen. nov., sp. nov., a methanotroph isolated from pond water.

    PubMed

    Hoefman, Sven; van der Ha, David; Iguchi, Hiroyuki; Yurimoto, Hiroya; Sakai, Yasuyoshi; Boon, Nico; Vandamme, Peter; Heylen, Kim; De Vos, Paul

    2014-06-01

    Two novel methanotrophic strains, R-49797(T) and OS501, were isolated from pond water in South Africa and Japan, respectively. Strains R-49797(T) and OS501 shared 99.7% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, non-motile cocci with a diplococcoid tendency and contained type I methanotroph intracytoplasmic membranes. The pmoA gene encoding particulate methane monooxygenase was present. Soluble methane monoooxygenase (sMMO) activity, the mmoX gene encoding sMMO and the nifH gene encoding nitrogenase were not detected. Methane and methanol were utilized as sole carbon source. The strains grew optimally at 25-33 C (range 20-37 C) and at pH 6.3-6.8 (range 5.8-9.0). The strains did not support growth in media supplemented with 1% (w/v) NaCl. For both strains, the two major fatty acids were C(16?:?1)?7c and C(16?:?0) and the DNA G+C content was 65.6 mol%. The isolates belong to the family Methylococcaceae of the class Gammaproteobacteria and cluster most closely among the genera Methylocaldum, Methylococcus and Methylogaea, with a 16S rRNA gene sequence similarity of 94.2% between strain R-49797(T) and its closest related type strain (Methylocaldum gracile VKM 14L(T)). Based on the low 16S rRNA gene sequence similarities with its nearest phylogenetic neighbouring genera, the formation of a separate lineage based on 16S rRNA and pmoA gene phylogenetic analysis, and the unique combination of phenotypic characteristics of the two isolated strains compared with the genera Methylocaldum, Methylococcus and Methylogaea, we propose to classify these strains as representing a novel species of a new genus, Methyloparacoccus murrellii gen. nov., sp. nov., within the family Methylococcaceae. The type strain of Methyloparacoccus murrellii is R-49797(T) (?=?LMG 27482(T)?=?JCM 19379(T)). PMID:24676728

  17. Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data

    PubMed Central

    Breinholt, Jesse W.; Kawahara, Akito Y.

    2013-01-01

    Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions. PMID:24148944

  18. Gen-2 RFID compatible, zero down-time, programmable mechanical strain-monitors and mechanical impact detectors

    NASA Astrophysics Data System (ADS)

    Chakrabartty, Shantanu; Feng, Tao; Aono, Kenji

    2013-04-01

    A key challenge in structural health monitoring (SHM) sensors embedded inside civil structures is that elec- tronics need to operate continuously such that mechanical events of interest can be detected and appropriately analyzed. Continuous operation however requires a continuous source of energy which cannot be guaranteed using conventional energy scavenging techniques. The paper describes a hybrid energy scavenging SHM sensor which experiences zero down-time in monitoring mechanical events of interest. At the core of the proposed sensor is an analog floating-gate storage technology that can be precisely programmed at nano-watt and pico- watt power levels. This facilitates self-powered, non-volatile data logging of the mechanical events of interest by scavenging energy directly from the mechanical events itself. Remote retrieval of the stored data is achieved using a commercial off-the-shelf Gen-2 radio-frequency identification (RFID) reader which periodically reads an electronic product code (EPC) that encapsulates the sensor data. The Gen-2 interface also facilitates in simultaneous remote access to multiple sensors and also facilitates in determining the range and orientation of the sensor. The architecture of the sensor is based on a token-ring topology which enables sensor channels to be dynamically added or deleted through software control.

  19. Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.

    PubMed

    Koeck, Daniela E; Ludwig, Wolfgang; Wanner, Gerhard; Zverlov, Vladimir V; Liebl, Wolfgang; Schwarz, Wolfgang H

    2015-08-01

    Phenotypic and phylogenetic studies were performed on new isolates of a novel Gram-stain-positive, anaerobic, non-sporulating, rod-shaped bacterium isolated from a thermophilic biogas plant. The novel organisms were able to degrade crystalline cellulose. 16S rRNA gene comparative sequence analysis demonstrated that the isolates formed a hitherto unknown subline within the family Lachnospiraceae. As a representative of the whole group of isolates, strain T3/55T was further characterized. The closest relative of T3/55T among the taxa with validly published names is Mobilitalea sibirica, sharing 93.9% 16S rRNA gene sequence similarity. Strain T3/55T was catalase-negative, indole-negative, and produced acetate, ethanol and propionic acid as major end products from cellulose metabolism. The major cellular fatty acids (>1%) were 16?:?0 dimethyl acetal, 16?:?0 fatty acid methyl ester and 16?:?0 aldehyde. The DNA G+C content was 36.6?mol%. A novel genus and species, Herbinix hemicellulosilytica gen. nov., sp. nov., is proposed based on phylogenetic analysis and physiological properties of the novel isolate. Strain T3/55T (?=?DSM 29228T?=?CECT 8801T), represents the type strain of Herbinix hemicellulosilytica gen. nov., sp. nov. PMID:25872956

  20. Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum Synergistetes isolated from the human oral cavity

    PubMed Central

    Downes, Julia; Vartoukian, Sonia R.; Dewhirst, Floyd E.; Izard, Jacques; Chen, Tsute; Yu, Wen-Han; Sutcliffe, Iain C.; Wade, William G.

    2009-01-01

    Four strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any species with validly published names. 16S rRNA and 23S rRNA gene sequence analyses and DNADNA reassociation data revealed that the strains constituted a novel group within the phylum Synergistetes and were most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455T and were sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and novel species, Pyramidobacter piscolens gen. nov., sp. nov., is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic, non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenylacetic acids as end products of metabolism. P. piscolens gen. nov., sp. nov. produced hydrogen sulphide but was otherwise largely biochemically unreactive. Growth was stimulated by the addition of glycine to broth media. The G+C content of the DNA of the type strain was 59?mol%. The type strain of Pyramidobacter piscolens sp. nov. is W5455T (=DSM 21147T=CCUG 55836T). PMID:19406777

  1. Genome sequence and description of Timonella senegalensis gen. nov., sp. nov., a new member of the suborder Micrococcinae

    PubMed Central

    Mishra, Ajay Kumar; Lagier, Jean-Christophe; Robert, Catherine; Raoult, Didier; Fournier, Pierre-Edouard

    2013-01-01

    Timonella senegalensis strain JC301T gen. nov., sp. nov. is the type strain of T. senegalensis gen. nov., sp. nov., a new species within the newly proposed genus Timonella. This bacterial strain was isolated from the fecal flora of a healthy Senegalese patient. In this report, we detail the features of this organism, together with the complete genome sequence and annotation. Timonella senegalensis strain JC301T exhibits the highest 16S rRNA similarity (95%) with Sanguibacter marinus, the closest validly published bacterial species. The genome of T. senegalensis strain JC301T is 3,010,102-bp long, with one chromosome and no plasmid. The genome contains 2,721 protein-coding genes and 72 RNA genes, including 5 rRNA genes. The genomic annotation revealed that T. senegalensis strain JC301T possesses the complete complement of enzymes necessary for the de novo biosynthesis of amino acids and vitamins (except for riboflavin and biotin), as well as the enzymes involved in the metabolism of various carbon sources, chaperone genes, and genes involved in the regulation of polyphosphate and glycogen levels. PMID:23991262

  2. A Controller-in-the Loop Simulation of Ground-Based Automated Separation Assurance in a NextGen Environment

    NASA Technical Reports Server (NTRS)

    Homola, J.; Prevot, Thomas; Mercer, Joey S.; Brasil, Connie L.; Martin, Lynne Hazel; Cabrall, C.

    2010-01-01

    A controller-in-the-loop simulation was conducted in the Airspace Operations Laboratory (AOL) at the NASA Ames Research Center to investigate the functional allocation aspects associated with ground-based automated separation assurance in a far-term NextGen environment. In this concept, ground-based automation handled the detection and resolution of strategic and tactical conflicts and alerted the controller to deferred situations. The controller was responsible for monitoring the automation and managing situations by exception. This was done in conditions both with and without arrival time constraints across two levels of traffic density. Results showed that although workload increased with an increase in traffic density, it was still manageable in most situations. The number of conflicts increased similarly with a related increase in the issuance of resolution clearances. Although over 99% of conflicts were resolved, operational errors did occur but were tied to local sector complexities. Feedback from the participants revealed that they thought they maintained reasonable situation awareness in this environment, felt that operations were highly acceptable at the lower traffic density level but were less so as it increased, and felt overall that the concept as it was introduced here was a positive step forward to accommodating the more complex environment envisioned as part of NextGen.

  3. Film and Language Learning in Victorian Schools: A Study of the 2009 Next Gen Program of the "Melbourne International Film Festival"

    ERIC Educational Resources Information Center

    Lo Bianco, Hana

    2010-01-01

    This article investigates the role of film in language education based on a study of the 2009 "Melbourne International Film Festival" (MIFF). It is structured around a literature review and results from surveys of students and teachers who participated in the young people's section of the program, Next Gen. The article argues that film can provide

  4. Film and Language Learning in Victorian Schools: A Study of the 2009 Next Gen Program of the "Melbourne International Film Festival"

    ERIC Educational Resources Information Center

    Lo Bianco, Hana

    2010-01-01

    This article investigates the role of film in language education based on a study of the 2009 "Melbourne International Film Festival" (MIFF). It is structured around a literature review and results from surveys of students and teachers who participated in the young people's section of the program, Next Gen. The article argues that film can provide…

  5. CHROMOSOMAL MAPPING OF 12 GENE-ASSOCIATED MARKERS IN CATTLE IDENTIFIES NOVEL REGIONS OF CONSERVED SYNTENY BETWEEN THE HUMAN AND BOVINE GEN0MES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Current gene density on the bovine genetic maps is extremely limited and the resolution of the human-bovine comparative map is insufficient for selection of positional candidate genes controlling many economic traits of interest in dairy cattle. This study describes the chromosomal mapping of 12 gen...

  6. El NCI inicia un estudio para evaluar la utilidad de la secuenciación genética para mejorar los resu

    Cancer.gov

    El Instituto Nacional del Cáncer (NCI) lanzará este mes un estudio clínico piloto denominado M-PACT con la finalidad de evaluar si el tratamiento asignado según mutaciones genéticas específicas puede brindar beneficios a pacientes con tumores sólidos meta

  7. Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P.

    PubMed

    Sumida, Tomomi; Yanagisawa, Tatsuo; Ishii, Ryohei; Yokoyama, Shigeyuki

    2010-09-01

    GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, was overexpressed in E. coli, purified by three chromatographic steps and cocrystallized with a lysyl adenylate analogue (LysAMS) by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The GenX-LysAMS crystals belonged to the triclinic space group P1, with unit-cell parameters a=54.80, b=69.15, c=94.08 A, alpha=95.47, beta=106.51, gamma=90.46 degrees, and diffracted to 1.9 A resolution. Furthermore, GenX was cocrystallized with translation elongation factor P (EF-P), which is believed to be a putative substrate of GenX, and LysAMS using PEG 4000 and ammonium sulfate as precipitants. The GenX-EF-P-LysAMS crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a=105.93, b=102.96, c=119.94 A, beta=99.4 degrees, and diffracted to 2.5 A resolution. Structure determination of the E. coli GenX-LysAMS and GenX-EF-P-LysAMS complexes by molecular replacement was successful and structure refinements are now in progress. PMID:20823541

  8. Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P

    PubMed Central

    Sumida, Tomomi; Yanagisawa, Tatsuo; Ishii, Ryohei; Yokoyama, Shigeyuki

    2010-01-01

    GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, was overexpressed in E. coli, purified by three chromatographic steps and cocrystallized with a lysyl adenylate analogue (LysAMS) by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The GenXLysAMS crystals belonged to the triclinic space group P1, with unit-cell parameters a=54.80, b = 69.15, c=94.08?, ? = 95.47, ? = 106.51, ? = 90.46, and diffracted to 1.9? resolution. Furthermore, GenX was cocrystallized with translation elongation factor P (EF-P), which is believed to be a putative substrate of GenX, and LysAMS using PEG 4000 and ammonium sulfate as precipitants. The GenXEF-PLysAMS crystals belonged to the monoclinic space group P21, with unit-cell parameters a= 105.93, b = 102.96, c = 119.94?, ? = 99.4, and diffracted to 2.5? resolution. Structure determination of the E. coli GenXLysAMS and GenXEF-PLysAMS complexes by molecular replacement was successful and structure refinements are now in progress. PMID:20823541

  9. Toxopsis calypsus gen. nov., sp. nov. (Cyanobacteria, Nostocales) from cave 'Francthi', Peloponnese, Greece: a morphological and molecular evaluation.

    PubMed

    Lamprinou, V; Skaraki, K; Kotoulas, G; Economou-Amilli, A; Pantazidou, A

    2012-12-01

    Representatives of a new cyanobacterial genus, Toxopsis Lamprinou & Pantazidou gen. nov., were found in fresh material from Cave 'Francthi' (Peloponnese, Greece) and isolated in cultures. Ecological data relating to the environmental parameters of the sampling sites are provided, such as the photosynthetically active radiation (PAR), temperature and relative humidity. Morphological characteristics and the life cycle of the type species Toxopsis calypsus Lamprinou & Pantazidou sp. nov. were studied using light microscopy and scanning and transmission microscopy. Molecular analysis based on the 16S rRNA gene sequence was also conducted. Toxopsis calypsus sp. nov. is a false-branched nostocalean cyanobacterium with both isopolar and heteropolar filaments bearing mono-pored and bi-pored heterocysts, and also hormogonia and akinetes. Isopolar filaments adhere by the centre to the substrate and are found mainly in fresh material and in young cultures; heteropolar filaments bearing a basic mono-pore heterocyst are dominant in aged (more than one-year-old) cultures. According to the revised taxonomic classification system of Komrek & Anagnostidis (1989) [Komrek, J. & Anagnostidis, K. (1989). Algol Stud, 56, 247-345] based mainly on morphological data, the new genus described here shares morphological characters with both nostocalean families Scytonemataceae and Microchaetaceae, showing similarities in particular to Scytonematopsis contorta [Vaccarino, M. A. & Johansen, J. R. (2011). Fottea 11, 149-161], Microchaetaceae. Molecular data from the 16S rRNA sequence determined in this paper showed that Toxopsis calypsus sp. nov. is more related to the family Microchaetaceae, and the five phylotypes analysed by PCR showed that the closest nostocalean relatives are Tolypothrix distorta SAG 93.79 (GenBank accession no. GQ287651) and Coleodesmium sp. ANT.L52B.5 (AY493596) with 95-96% and 96% similarity, respectively. In contrast, the five phylotypes showed a distant similarity to Scytonematopsis contorta (<91%). The phenotypic and genetic traits strongly supported the classification of the five phylotypes as a new taxon for which the name Toxopsis calypsus Lamprinou & Pantazidou gen. nov., sp. nov. is proposed. PMID:22247210

  10. Progress reports for Gen IV sodium fast reactor activities FY 2007.

    SciTech Connect

    Cahalan, J. E.; Tentner, A. M.; Nuclear Engineering Division

    2007-10-04

    An important goal of the US DOE Sodium Fast Reactor (SFR) program is to develop the technology necessary to increase safety margins in future fast reactor systems. Although no decision has been made yet about who will build the next demonstration fast reactor, it seems likely that the construction team will include a combination of international companies, and the safety design philosophy for the reactor will reflect a consensus of the participating countries. A significant amount of experience in the design and safety analysis of Sodium Fast Reactors (SFR) using oxide fuel has been developed in both Japan and France during last few decades. In the US, the traditional approach to reactor safety is based on the principle of defense-in-depth, which is usually expressed in physical terms as multiple barriers to release of radioactive material (e.g. cladding, reactor vessel, containment building), but it is understood that the 'barriers' may consist of active systems or even procedures. As implemented in a reactor design, defense-in-depth is classed in levels of safety. Level 1 includes measures to specify and build a reliable design with significant safety margins that will perform according to the intentions of the designers. Level 2 consists of additional design measures, usually active systems, to protect against unlikely accidental events that may occur during the life of the plant. Level 3 design measures are intended to protect the public in the event of an extremely unlikely accident not foreseen to occur during the plant's life. All of the design measures that make up the first three levels of safety are within the design basis of the plant. Beyond Level 3, and beyond the normal design basis, there are accidents that are not expected to occur in a whole generation of plants, and it is in this class that severe accidents, i.e. accidents involving core melting, are included. Beyond design basis measures to address severe accidents are usually identified as being for prevention of progression into severe accident conditions (prevention of core melting) or for mitigation of severe accident consequences (mitigation of the impact of core melting to protect public health and safety). Because design measures for severe accident prevention and mitigation are beyond the normal design basis, established regulatory guidelines and codes do not provide explicit identification of the design performance requirements for severe accident accommodation. The treatment of severe accidents is one of the key issues of R&D plans for the Gen IV systems in general, and for the Sodium Fast Reactor (SFR) in particular. Despite the lack of an unambiguous definition of safety approach applicable for severe accidents, there is an emerging consensus on the need for their consideration for the design. The US SFR program and Argonne National Laboratory (ANL) in particular have actively studied the potential scenarios and consequences of Hypothetical Core Disruptive Accidents (HCDA) for SFRs with oxide fuel during the Fast Flux Test Facility (FFTF) and Clinch River Breeder Reactor Plant (CRBRP) programs in the 70s and 80s. Later, the focus of the US SFR safety R&D activities shifted to the prevention of all HCDAs through passive safety features of the SFRs with metal fuel in the Integral Fast Reactor (IFR) program, and the study of severe accident consequences was de-emphasized. The goal of this paper is to provide an overview of the current SFR safety approach and the role of severe accidents in Japan and France, in preparation for an expected and more active collaboration in this area between the US, Japan, and France.

  11. Plastorhodobacter daqingensis gen. nov., sp. nov.: a non-phototrophic bacterium isolated from Daqing Oilfield.

    PubMed

    Xie, Bai-Sheng; Lv, Xiang-Lin; Cai, Man; Tang, Yue-Qin; Wang, Ya-Nan; Cui, Heng-Lin; Liu, Xue-Ying; Tan, Yan; Wu, Xiao-Lei

    2015-05-01

    Two aerobic Gram staining negative, non-motile, and rod-shaped strains, DQW12E81-30(T) and DQW12E6-37-1, were isolated from an oil production mixture from Daqing Oilfield, northeastern China. Phylogenetic analysis based on the nearly complete 16S rRNA gene sequences revealed that strains DQW12E81-30(T) and DQW12E6-37-1 were members of family Rhodobacteraceae, which showed 95.6-95.9 % of 16S rRNA gene sequence similarities with Pararhodobacter aggregans DSM 18938(T), Rhodobacter veldkampii CGMCC 1.5006(T), and Roseinatronobacter thiooxidans DSM 13087(T), and lower similarities (<95.1 %) with all the left type species. Growth of strains DQW12E81-30(T) and DQW12E6-37-1 occurred at pH 7-8, 15-45 C, and 0-4 % (w/v) of NaCl. The strains could grow both in dark and in light, but neither photosynthetic pigments nor photosynthetic reaction center gene pufM were detected in the strains. These photosynthesis-related features of the two isolates were different from those of Rhodobacter and Roseinatronobacter bacteria, but similar with those of Pararhodobacter. The genomic DNA G+C contents of strains DQW12E81-30(T) and DQW12E6-37-1 were 66.9 and 63.7 mol%, respectively. The predominant ubiquinone was Q-10 for both the strains. The major polar lipids of strain DQW12E81-30(T) were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, unidentified aminolipid, unidentified glycolipid, and unidentified phospholipid. The two strains had C18:1 ?7c, C18:0, and C18:1 ?7c 11-methyl as the major fatty acids. In addition, the strains DQW12E81-30(T) and DQW12E6-37-1 had C16:1 ?7c/C16:1 ?6c, C12:0, C14:0, C14:0 3-OH/C16:1 iso I, C10:0 3-OH, which were remarkably different from those of Pararhodobacter and Roseinatronobacter. The results of phenotypic, genotypic, and chemotaxonomic characteristics analyses indicated that strains DQW12E81-30(T) and DQW12E6-37-1 were readily different from their most phylogenetically closely related genera. Plastorhodobacter daqingensis gen. nov, sp. nov. is proposed for strains DQW12E81-30(T) and DQW12E6-37-1. The type strain is DQW12E81-30(T) (=LMG 27732(T)=CGMCC 1.12750(T)). PMID:25572494

  12. Mooreia alkaloidigena gen. nov., sp. nov. and Catalinimonas alkaloidigena gen. nov., sp. nov., alkaloid-producing marine bacteria in the proposed families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. in the phylum Bacteroidetes.

    PubMed

    Choi, Eun Ju; Beatty, Deanna S; Paul, Lauren A; Fenical, William; Jensen, Paul R

    2013-04-01

    Bacterial strains CNX-216(T) and CNU-914(T) were isolated from marine sediment samples collected from Palmyra Atoll and off Catalina Island, respectively. Both strains were gram-negative and aerobic and produce deep-orange to pink colonies and alkaloid secondary metabolites. Cells of strain CNX-216(T) were short, non-motile rods, whereas cells of strain CNU-914(T) were short, curved rods with gliding motility. The DNA G+C contents of CNX-216(T) and CNU-914(T) were respectively 57.7 and 44.4 mol%. Strains CNX-216(T) and CNU-914(T) contained MK-7 as the predominant menaquinone and iso-C15?:?0 and C16?:?1?5c as the major fatty acids. Phylogenetic analyses revealed that both strains belong to the order Cytophagales in the phylum Bacteroidetes. Strain CNX-216(T) exhibited low 16S rRNA gene sequence identity (87.1?%) to the nearest type strain, Cesiribacter roseus 311(T), and formed a well-supported lineage that is outside all currently described families in the order Cytophagales. Strain CNU-914(T) shared 97.6?% 16S rRNA gene sequence identity with 'Porifericola rhodea' N5EA6-3A2B and, together with 'Tunicatimonas pelagia' N5DB8-4 and four uncharacterized marine bacteria isolated as part of this study, formed a lineage that is clearly distinguished from other families in the order Cytophagales. Based on our polyphasic taxonomic characterization, we propose that strains CNX-216(T) and CNU-914(T) represent novel genera and species, for which we propose the names Mooreia alkaloidigena gen. nov., sp. nov. (type strain CNX-216(T) ?=?DSM 25187(T) ?=?KCCM 90102(T)) and Catalinimonas alkaloidigena gen. nov., sp. nov. (type strain CNU-914(T) ?=?DSM 25186(T) ?=?KCCM 90101(T)) within the new families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. PMID:22753528

  13. Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively.

    PubMed

    Xie, Cheng-Hui; Yokota, Akira

    2005-11-01

    The aim of this study was to clarify the taxonomic position of the nitrogen-fixing and hydrogen-oxidizing bacteria Alcaligenes latus strains IAM 12599T, IAM 12664 and IAM 12665 and Pseudomonas saccharophila IAM 14368T. It was found that the type strain of Alcaligenes latus, IAM 12599T, showed 99 x 9 and 96 x 1 % 16S rRNA gene sequence similarity to strains IAM 12665 and IAM 12664, respectively. A comparison using DNA-DNA hybridization suggested that strains IAM 12599T and IAM 12665 belong to a single species (89 x 7 %) and that strain IAM 12664 (35 x 1 %) forms a separate species. The phenotypic characteristics also support the conclusion that these bacteria should be identified as two species of a new genus: Azohydromonas lata gen. nov., comb. nov. (type strain IAM 12599T=DSM 1122T=LMG 3321T=ATCC 29712T; reference strain IAM 12665=DSM 1123=LMG 3325=ATCC 29714) and Azohydromonas australica sp. nov. (type strain IAM 12664T=DSM 1124T=LMG 3324T=ATCC 29713T). Pseudomonas saccharophila IAM 14368T was found to be closely related to the phototrophic bacterium Roseateles depolymerans, with 96 x 8 % 16S rRNA gene sequence similarity, but the two bacteria are quite different with respect to their metabolism and some significant phenotypic characteristics, suggesting that they cannot be included in a single genus. Further studies on their nifH gene sequences, G+C content of the DNA and cellular fatty acid composition confirm that Pseudomonas saccharophila should be reclassified: the name Pelomonas saccharophila gen. nov., comb. nov. is proposed, with the type strain IAM 14368T (=LMG 2256T=ATCC 15946T). PMID:16280506

  14. Youngimonas vesicularis gen. nov., sp. nov., of the family Rhodobacteraceae, isolated from surface seawater, reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. and emended description of the genus Donghicola Yoon et al. 2007.

    PubMed

    Hameed, Asif; Shahina, Mariyam; Lin, Shih-Yao; Nakayan, Phanit; Liu, You-Cheng; Lai, Wei-An; Hsu, Yi-Han

    2014-08-01

    A Gram-staining-negative, non-pigmented, strictly aerobic, rod-shaped, non-spore-forming, non-motile bacterium, devoid of bacteriochlorophyll, designated strain CC-AMW-E(T), was isolated from surface seawater off the coast at Kending, Taiwan. Strain CC-AMW-E(T) shared 95.7 and 93.9% 16S rRNA gene sequence similarity, respectively, with the type strains of the type species of the genera Donghicola (Donghicola eburneus SW-277(T)) and Roseovarius (Roseovarius tolerans EL-172(T)). The predominant (>75% of the total) fatty acid was summed feature 8 (C(18?:?1)?6c and/or C(18?:?1)?7c). The polar lipid profile included major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified aminolipid. In addition, moderate amounts of an unidentified lipid and trace amounts of an unidentified phospholipid were detected. The DNA G+C content was 67.9 mol%. Ubiquinone Q-10 was the sole respiratory quinone. Based on its phylogenetic distinctiveness and distinguishing phenotypic characteristics (in particular its polar lipid pattern), we conclude that strain CC-AMW-E(T) represents a novel genus and species of the family Rhodobacteraceae, for which the name Youngimonas vesicularis gen. nov., sp. nov. is proposed. The type strain of Youngimonas vesicularis is CC-AMW-E(T) (?=?JCM 18819(T)?=?BCRC 80549(T)). In addition, an emended description of the genus Donghicola Yoon et al. 2007 and the reclassification of Donghicola xiamenensis Tan et al. 2009 as Pseudodonghicola xiamenensis gen. nov., comb. nov. (type strain Y-2(T)?=?MCCC 1A00107(T)?=?LMG 24574(T)?=?CGMCC 1.7081(T)) are proposed. PMID:24844264

  15. Measurements of the neutron electric to magnetic form factor ratio GEn/GMn via the 2H(e→,e'n→)1H reaction to Q2=1.45 (GeV/c)2

    NASA Astrophysics Data System (ADS)

    Plaster, B.; Semenov, A. Yu.; Aghalaryan, A.; Crouse, E.; MacLachlan, G.; Tajima, S.; Tireman, W.; Ahmidouch, A.; Anderson, B. D.; Arenhövel, H.; Asaturyan, R.; Baker, O. K.; Baldwin, A. R.; Barkhuff, D.; Breuer, H.; Carlini, R.; Christy, E.; Churchwell, S.; Cole, L.; Danagoulian, S.; Day, D.; Eden, T.; Elaasar, M.; Ent, R.; Farkhondeh, M.; Fenker, H.; Finn, J. M.; Gan, L.; Gasparian, A.; Garrow, K.; Gueye, P.; Howell, C. R.; Hu, B.; Jones, M. K.; Kelly, J. J.; Keppel, C.; Khandaker, M.; Kim, W.-Y.; Kowalski, S.; Lung, A.; Mack, D.; Madey, R.; Manley, D. M.; Markowitz, P.; Mitchell, J.; Mkrtchyan, H.; Opper, A. K.; Perdrisat, C.; Punjabi, V.; Raue, B.; Reichelt, T.; Reinhold, J.; Roche, J.; Sato, Y.; Savvinov, N.; Semenova, I. A.; Seo, W.; Simicevic, N.; Smith, G.; Stepanyan, S.; Tadevosyan, V.; Tang, L.; Taylor, S.; Ulmer, P. E.; Vulcan, W.; Watson, J. W.; Wells, S.; Wesselmann, F.; Wood, S.; Yan, Chen; Yan, Chenyu; Yang, S.; Yuan, L.; Zhang, W.-M.; Zhu, H.; Zhu, X.

    2006-02-01

    We report values for the neutron electric to magnetic form factor ratio, GEn/GMn, deduced from measurements of the neutron's recoil polarization in the quasielastic 2H(e→,e'n→)1H reaction, at three Q2 values of 0.45, 1.13, and 1.45 (GeV/c)2. The data at Q2=1.13 and 1.45 (GeV/c)2 are the first direct experimental measurements of GEn employing polarization degrees of freedom in the Q2>1 (GeV/c)2 region and stand as the most precise determinations of GEn for all values of Q2.

  16. Third-Party Evaluation of Petro Tex Hydrocarbons, LLC, ReGen Lubricating Oil Re-refining Process

    SciTech Connect

    Compere, A L; Griffith, William {Bill} L

    2009-04-01

    This report presents an assessment of market, energy impact, and utility of the PetroTex Hydrocarbons, LLC., ReGen process for re-refining used lubricating oil to produce Group I, II, and III base oils, diesel fuel, and asphalt. PetroTex Hydrocarbons, LLC., has performed extensive pilot scale evaluations, computer simulations, and market studies of this process and is presently evaluating construction of a 23 million gallon per year industrial-scale plant. PetroTex has obtained a 30 acre site in the Texas Industries RailPark in Midlothian Texas. The environmental and civil engineering assessments of the site are completed, and the company has been granted a special use permit from the City of Midlothian and air emissions permits for the Texas Commission on Environmental Quality.

  17. A new genus and species (Cornucollis gen. n. masoalensis sp. n.) of praying mantis from northern Madagascar (Mantodea, Iridopterygidae, Tropidomantinae)

    PubMed Central

    Brannoch, Sydney K.; Svenson, Gavin J.

    2016-01-01

    Abstract An examination of Malagasy specimens accessed within the Muséum national d’Histoire naturelle, Paris, France, produced a praying mantis (Insecta: Mantodea) of an undescribed genus and species. An investigation of the internal and external morphology, in addition to its collection locality, revealed that this specimen belongs to the Iridopterygidae subfamily Tropidomantinae. Furthermore, the specimen’s unique combination of characters justified the creation of a new genus. Geographic distributional records and external morphological character evidence are presented for Cornucollis gen. n. masoalensis sp. n. We provide a dichotomous key of the Tropidomantinae and Nilomantinae genera distributed within Madagascar. High-resolution images, illustrations of morphological characters, natural history information, and measurement data are presented. PMID:26877694

  18. Pseudofornicia gen. n. (Hymenoptera, Braconidae, Microgastrinae), a new Indo-Australian genus and one new species from Vietnam

    PubMed Central

    van Achterberg, Cornelis; Long, Khuat Dang; Chen, Xue-xin; You, Lan-shao

    2015-01-01

    Abstract Pseudofornicia gen. n. (Hymenoptera: Braconidae: Microgastrinae) is described (type species: Pseudofornicia nigrisoma sp. n. from Vietnam) including three Oriental (type species, Pseudofornicia flavoabdominis (He & Chen, 1994), comb. n. and Pseudofornicia vanachterbergi Long, (nom. n. for Fornicia achterbergi Long, 2007; not Fornicia achterbergi Yang & Chen, 2006) and one Australian species (Pseudofornicia commoni (Austin & Dangerfield, 1992), comb. n.). Keys to genera with similar metasomal carapace and to species of the new genus are provided. The new genus shares the curved inner middle tibial spur, the comparatively small head, the median carina of the first metasomal tergite and the metasomal carapace with Fornicia Brull, 1846, but has the first tergite movably joined to the second tergite and the third tergite 1.11.6 as long as the second tergite medially and is flattened in lateral view. One of the included species is a primary homonym and is renamed in this paper. PMID:26478707

  19. Revision of the genus Pelecinobaccha Shannon, description of Relictanum gen. nov., and redescription of Atylobaccha flukiella (Curran, 1941) (Diptera: Syrphidae).

    PubMed

    Miranda, Gil Felipe Gonalves; Marshall, Stephen A; Skevington, Jeffrey H

    2014-01-01

    Recent phylogenetic analyses of Ocyptamus Macquart, 1834 (Diptera, Syrphidae) confirmed the paraphyly of this genus and provided evidence to divide it into several monophyletic subgroups, of which the largest is the clade traditionally treated as the Ocyptamus tristis species group. This group is here redefined, divided into the genera Pelecinobaccha Shannon, 1927 and Relictanum gen. nov., and revised along with the closely related and newly resurrected genus Atylobaccha Hull, 1949. Twenty-four new species (22 in Pelecinobaccha and two in Relictanum) are described and 35 species (27 in Pelecinobaccha, seven in Relictanum and Atylobaccha flukiella Curran, 1941) are redescribed. Pelecinobaccha is divided into four species groups (P. adspersa species group, P. brevipennis species group, P. peruviana species group and P. susio species group). An identification key, illustrations and distribution maps for all species from this study are also presented. PMID:24943804

  20. Rhopalomma stefaniae gen. et sp. n., the first ommatid beetle from the Upper Jurassic in Australia (Coleoptera: Archostemata: Ommatidae).

    PubMed

    Ashman, Lauren G; Oberprieler, Rolf G; ?lipi?ski, Adam

    2015-01-01

    The first Upper Jurassic fossil of the family Ommatidae (Coleoptera: Archostemata) from Australia is described and illustrated from a single specimen discovered at the Talbragar Fish Bed. Rhopalomma stefaniae gen. et sp.n. is classified in Ommatidae based on the length and insertion of the antennae, the tuberculate cuticle, the pattern of elytral striae, the complete epipleura and the presence of scutellary strioles. Due to the lack of preservation of crucial characters, Rhopalomma cannot be assigned to a subfamily and is therefore classified as Ommatidae incertae sedis. Rhopalomma fills an important gap in the fossil record of the family, indicating that Ommatidae occurred in Australia from the Lower Jurassic to the present day. Australia is the only place in the world where this family is found in both the fossil record and the living fauna. PMID:26249943

  1. Taxonomic studies on a new marine ciliate, Apocoleps magnus gen. nov., spec. nov. (Ciliophora, Colepidae), isolated from Qingdao, China

    NASA Astrophysics Data System (ADS)

    Chen, Xiangrui; Warren, Alan; Song, Weibo

    2009-12-01

    The morphology and infraciliature of a new marine colepid ciliate, Apocoleps magnus gen. nov., spec. nov., are described based on living observations and silver impregnations. The new genus Apocoleps is characterized by having 8 (vs. 6 in most other related genera) armour tiers, spines at both ends of the cell, 3 adoral organelles and plates with 4 reniform uni-windows. Apocoleps magnus spec. nov. is defined by the following features: body elongated and slightly curved, about 100-120m 35-45 m in vivo; anterior tertiary tier plate with four uni-windows, most secondary and main tier plates with four uni-windows, posterior tertiary tier plate with two uni-windows; left plate margin slightly serrated; on average 23 transverse and 22 longitudinal ciliary rows; one terminal contractile vacuole; marine habitat.

  2. Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium.

    PubMed

    Tang, M; Chen, C; Li, J; Xiang, W; Wu, H; Wu, J; Dai, S; Wu, H; Li, T; Wang, G

    2016-02-01

    A Gram-stain-negative, red, non-spore-forming, strictly aerobic bacterium, designated strain A4T, was isolated from culture broth of a marine cyanobacterium. Cells were flexible rods with gliding motility. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain A4T formed a coherent cluster with members of the genera Roseivirga and Fabibacter, and represents a distinct lineage in the family Flammeovirgaceae. Thermotolerance and a distinctive cellular fatty acid profile could readily distinguish this isolate from any bacteria of the genera Roseivirga and Fabibacter with a validly published name. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain A4T is suggested to represent a novel species in a novel genus, for which the name Fabivirga thermotolerans gen. nov., sp. nov. is proposed. The type strain is A4T ( = KCTC 42507T = CGMCC 1.15111T). PMID:26652750

  3. A new genus and species (Cornucollis gen. n. masoalensis sp. n.) of praying mantis from northern Madagascar (Mantodea, Iridopterygidae, Tropidomantinae).

    PubMed

    Brannoch, Sydney K; Svenson, Gavin J

    2016-01-01

    An examination of Malagasy specimens accessed within the Musum national d'Histoire naturelle, Paris, France, produced a praying mantis (Insecta: Mantodea) of an undescribed genus and species. An investigation of the internal and external morphology, in addition to its collection locality, revealed that this specimen belongs to the Iridopterygidae subfamily Tropidomantinae. Furthermore, the specimen's unique combination of characters justified the creation of a new genus. Geographic distributional records and external morphological character evidence are presented for Cornucollis gen. n. masoalensis sp. n. We provide a dichotomous key of the Tropidomantinae and Nilomantinae genera distributed within Madagascar. High-resolution images, illustrations of morphological characters, natural history information, and measurement data are presented. PMID:26877694

  4. Leptohelia flexibilis gen. nov. et sp. nov., a remarkable deep-sea stylasterid (Cnidaria: Hydrozoa: Stylasteridae) from the southwest Pacific.

    PubMed

    Lindner, Alberto; Cairns, Stephen D; Zibrowius, Helmut

    2014-01-01

    Leptohelia flexibilis gen. nov. et sp. nov., the first stylasterid with a combined calcified and non-calcified skeleton, is described from seamounts and the slope off the islands of New Caledonia, in the southwestern Pacific. The new species is distinguished from all other species of the family Stylasteridae by having a non-calcified organic axis, internal to the basal portion of the calcified corallum. The internal axis is flexible and enclosed by a series of up to 10 calcified annuli, allowing passive lateral bending of the colony. Molecular phylogenetic analyses confirm that Leptohelia flexibilis is a stylasterid coral and reveal that the species is closely related to Leptohelia microstylus comb. nov., a southwestern Pacific stylasterid that lacks an internal axis. PMID:25543758

  5. Study of Gryllacridinae (Orthoptera: Stenopelmatidae) from Thailand and
    adjacent countries: the genera Ultragryllacris gen. nov. and Capnogryllacris.

    PubMed

    Gorochov, Andrej V; Dawwrueng, Pattarawich; Artchawakom, Taksin

    2015-01-01

    A new material on the genera Ultragryllacris gen. nov. and Capnogryllacris Karny, 1937 from Thailand, Laos and Cambodia is considered. Five new species and subspecies are described: U. pulchra sp. nov.; U. p. alboclypeata subsp. nov.; C. thaica sp. nov.; C. sakaerat sp. nov.; C. phaeocephala cambodiensis subsp. nov. Capnogryllacris s. l. is divided into two possible subgenera (Capnogryllacris s. str. and Dictyogryllacris Karny, 1937, stat. nov.) as a minimum; the former genera Borneogryllacris Karny, 1937, syn. nov., Marthogryllacris Karny, 1937, syn. nov. and Erythrogryllacris Karny, 1937, syn. nov. are treated as synonyms of the subgenus Capnogryllacris. Previously unknown female for C. khmerica Gorochov, 2003 is described; neotype for C. martha (Griffini, 1914 ), type species of Marthogryllacris, is designated; C. erythrocephala Gorochov, 2003, sp. ressur. and C. e. borealis Gorochov, 2003, stat. ressur. are restored from synonyms of C. martha and from species status, respectively. PMID:26624154

  6. Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma).

    PubMed

    Liu, Alexander G; Matthews, Jack J; Menon, Latha R; McIlroy, Duncan; Brasier, Martin D

    2014-10-22

    Muscle tissue is a fundamentally eumetazoan attribute. The oldest evidence for fossilized muscular tissue before the Early Cambrian has hitherto remained moot, being reliant upon indirect evidence in the form of Late Ediacaran ichnofossils. We here report a candidate muscle-bearing organism, Haootia quadriformis n. gen., n. sp., from approximately 560 Ma strata in Newfoundland, Canada. This taxon exhibits sediment moulds of twisted, superimposed fibrous bundles arranged quadrilaterally, extending into four prominent bifurcating corner branches. Haootia is distinct from all previously published contemporaneous Ediacaran macrofossils in its symmetrically fibrous, rather than frondose, architecture. Its bundled fibres, morphology, and taphonomy compare well with the muscle fibres of fossil and extant Cnidaria, particularly the benthic Staurozoa. Haootia quadriformis thus potentially provides the earliest body fossil evidence for both metazoan musculature, and for Eumetazoa, in the geological record. PMID:25165764

  7. Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef.

    PubMed

    Obornk, Miroslav; Modr, David; Luke, Martin; Cernotkov-St?brn, Eva; Cihl?, Jaromr; Tesa?ov, Martina; Kotabov, Eva; Vancov, Marie; Pril, Ond?ej; Luke, Julius

    2012-03-01

    Chromerida are photoautotrophic alveolates so far only isolated from corals in Australia. It has been shown that these secondary plastid-containing algae are closely related to apicomplexan parasites and share various morphological and molecular characters with both Apicomplexa and Dinophyta. So far, the only known representative of the phylum was Chromera velia. Here we provide a formal description of another chromerid, Vitrella brassicaformis gen. et sp. nov., complemented with a detailed study on its ultrastructure, allowing insight into its life cycle. The novel alga differs significantly from the related chromerid C. velia in life cycle, morphology as well as the plastid genome. Analysis of photosynthetic pigments on the other hand demonstrate that both chromerids lack chlorophyll c, the hallmark of phototrophic chromalveolates. Based on the relatively high divergence between C. velia and V. brassicaformis, we propose their classification into distinct families Chromeraceae and Vitrellaceae. Moreover, we predict a hidden and unexplored diversity of the chromerid algae. PMID:22055836

  8. Haootia quadriformis n. gen., n. sp., interpreted as a muscular cnidarian impression from the Late Ediacaran period (approx. 560 Ma)

    PubMed Central

    Liu, Alexander G.; Matthews, Jack J.; Menon, Latha R.; McIlroy, Duncan; Brasier, Martin D.

    2014-01-01

    Muscle tissue is a fundamentally eumetazoan attribute. The oldest evidence for fossilized muscular tissue before the Early Cambrian has hitherto remained moot, being reliant upon indirect evidence in the form of Late Ediacaran ichnofossils. We here report a candidate muscle-bearing organism, Haootia quadriformis n. gen., n. sp., from approximately 560 Ma strata in Newfoundland, Canada. This taxon exhibits sediment moulds of twisted, superimposed fibrous bundles arranged quadrilaterally, extending into four prominent bifurcating corner branches. Haootia is distinct from all previously published contemporaneous Ediacaran macrofossils in its symmetrically fibrous, rather than frondose, architecture. Its bundled fibres, morphology, and taphonomy compare well with the muscle fibres of fossil and extant Cnidaria, particularly the benthic Staurozoa. Haootia quadriformis thus potentially provides the earliest body fossil evidence for both metazoan musculature, and for Eumetazoa, in the geological record. PMID:25165764

  9. Comparison of Fracture Gradient Methods for the FutureGen 2.0 Carbon Storage Site, Ill., USA.

    NASA Astrophysics Data System (ADS)

    Appriou, D.; Spane, F.; Wurstner White, S.; Kelley, M. E.; Sullivan, E. C.; Bonneville, A.; Gilmore, T. J.

    2014-12-01

    As part of a first-of-its-kind carbon dioxide storage project, FutureGen Industrial Alliance is planning to inject 1.1 MMt/yr of supercritical CO2 over a 20-year period within a 1240 m deep saline aquifer (Mount Simon Sandstone) located in Morgan County, Illinois, USA. Numerous aspects of the design and operational activities of the CO2 storage site are dependent on the geomechanical properties of the targeted reservoir zone, as well as of the overlying confining zone and the underlying crystalline Precambrian basement. Detailed determination of the state-of-stress within the subsurface is of paramount importance in successfully designing well drilling/completion aspects, as well as assessing the risk of induced seismicity and the potential for creating and/or reopening pre-existing fractures; all of which help ensure the safe long-term storage of injected CO2. The quantitative determination of the subsurface fracture gradient is one of the key geomechanical parameters for the site injection design and operational limits (e.g., maximum safe injection pressure). A characterization well drilled in 2011 provides subsurface geomechanical characterization information for the FutureGen 2.0 site, and includes: 1) continuous elastic properties inferred from sonic/acoustic wireline logs 2) discrete depth geomechanical laboratory core measurements and 3) results obtained from hydraulic fracturing tests of selected borehole/depth-intervals. In this paper, the precise fracture gradients derived from borehole geomechanical test results are compared with semi-empirical, fracture gradient calculation/relationships based on elastic property wireline surveys and laboratory geomechanical core test results. Implications for using various fracture-gradients obtained from the different methods are assessed using PNNL's subsurface multiphase flow and transport simulator STOMP-CO2. The implications for operational activities at the site (based on using different fracture gradients) are also discussed.

  10. FutureGen 2.0 Monitoring Program: An Overview of the Monitoring Approach and Technologies Selected for Implementation

    SciTech Connect

    Vermeul, Vince R.; Strickland, Chris E.; Thorne, Paul D.; Bjornstad, Bruce N.; Mackley, Rob D.; Kelly, Mark E.; Sullivan, Charlotte; Williams, Mark D.; Amonette, James E.; Downs, Janelle L.; Fritz, Brad G.; Szecsody, Jim E.; Bonneville, Alain; Gilmore, Tyler J.

    2014-12-31

    The FutureGen 2.0 Project will design and build a first-of-its-kind, near-zero emissions coal-fueled power plant with carbon capture and storage (CCS). To assess storage site performance and meet the regulatory requirements of the Class VI Underground Injection Control (UIC) Program for CO2 Geologic Sequestration, the FutureGen 2.0 project will implement a suite of monitoring technologies designed to 1) evaluate CO2 mass balance and 2) detect any unforeseen loss in CO2 containment. The monitoring program will include direct monitoring of the injection stream and reservoir, and early-leak-detection monitoring directly above the primary confining zone. It will also implement an adaptive monitoring strategy whereby monitoring results are continually evaluated and the monitoring network is modified as required, including the option to drill additional wells in out-years. Wells will be monitored for changes in CO2 concentration and formation pressure, and other geochemical/isotopic signatures that provide indication of CO2 or brine leakage. Indirect geophysical monitoring technologies that were selected for implementation include passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture logging. Near-surface monitoring approaches that have been initiated include surficial aquifer and surface- water monitoring, soil-gas monitoring, atmospheric monitoring, and hyperspectral data acquisition for assessment of vegetation conditions. Initially, only the collection of baseline data sets is planned; the need for additional near- surface monitoring will be continually evaluated throughout the design and operational phases of the project, and selected approaches may be reinstituted if conditions warrant. Given the current conceptual understanding of the subsurface environment, early and appreciable impacts to near-surface environments are not expected.

  11. Enhanced/Synthetic Vision and Head-Worn Display Technologies for Terminal Maneuvering Area NextGen Operations

    NASA Technical Reports Server (NTRS)

    Arthur, Jarvis J., III; Prinzell, Lawrence J.; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

    2011-01-01

    NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

  12. Fukuyoa paulensis gen. et sp. nov., a new genus for the globular species of the dinoflagellate Gambierdiscus (Dinophyceae).

    PubMed

    Gómez, Fernando; Qiu, Dajun; Lopes, Rubens M; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi/G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov. PMID:25831082

  13. Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the Acidobacteria.

    PubMed

    Kulichevskaya, Irina S; Suzina, Natalia E; Liesack, Werner; Dedysh, Svetlana N

    2010-02-01

    Bryobacter aggregatus gen. nov., sp. nov. is proposed to accommodate three strains of slowly growing, chemo-organotrophic bacteria isolated from acidic Sphagnum peat bogs. These bacteria were strictly aerobic, Gram-negative, colourless, non-motile coccoids or short rods that multiplied by normal cell division and formed irregularly shaped cell aggregates. Strains MPL3(T), MPL1011 and MOB76 were acidotolerant, mesophilic organisms capable of growth at pH 4.5-7.2 and between 4 and 33 degrees C (optimum growth at pH 5.5-6.5 and 22-28 degrees C). The preferred growth substrates were sugars, some heteropolysaccharides and galacturonic and glucuronic acids, which are released during decomposition of Sphagnum moss. The major fatty acids were iso-C(15 : 0), C(16 : 0) and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c); the major quinones were MK-9 and MK-10. The DNA G+C content was 55.5-56.5 mol%. Strains MPL3(T), MPL1011 and MOB76 possessed nearly identical 16S rRNA gene sequences and belonged to the phylum Acidobacteria. They represent the first taxonomically characterized members of acidobacterial subdivision 3 and display only 81.7-86.7 % 16S rRNA gene sequence similarity to other members of the Acidobacteria with validly published names. Therefore, strains MPL3(T), MPL1011 and MOB76 are classified as representatives of a novel species in a new genus, for which the name Bryobacter aggregatus gen. nov., sp. nov. is proposed; strain MPL3(T) (=ATCC BAA-1390(T) =DSM 18758(T)) is the type strain of Bryobacter aggregatus. PMID:19651730

  14. Enhanced/synthetic vision and head-worn display technologies for terminal maneuvering area NextGen operations

    NASA Astrophysics Data System (ADS)

    Arthur, Jarvis J., III; Prinzel, Lawrence J., III; Williams, Steven P.; Bailey, Randall E.; Shelton, Kevin J.; Norman, R. Mike

    2011-06-01

    NASA is researching innovative technologies for the Next Generation Air Transportation System (NextGen) to provide a "Better-Than-Visual" (BTV) capability as adjunct to "Equivalent Visual Operations" (EVO); that is, airport throughputs equivalent to that normally achieved during Visual Flight Rules (VFR) operations rates with equivalent and better safety in all weather and visibility conditions including Instrument Meteorological Conditions (IMC). These new technologies build on proven flight deck systems and leverage synthetic and enhanced vision systems. Two piloted simulation studies were conducted to access the use of a Head-Worn Display (HWD) with head tracking for synthetic and enhanced vision systems concepts. The first experiment evaluated the use a HWD for equivalent visual operations to San Francisco International Airport (airport identifier: KSFO) compared to a visual concept and a head-down display concept. A second experiment evaluated symbology variations under different visibility conditions using a HWD during taxi operations at Chicago O'Hare airport (airport identifier: KORD). Two experiments were conducted, one in a simulated San Francisco airport (KSFO) approach operation and the other, in simulated Chicago O'Hare surface operations, evaluating enhanced/synthetic vision and head-worn display technologies for NextGen operations. While flying a closely-spaced parallel approach to KSFO, pilots rated the HWD, under low-visibility conditions, equivalent to the out-the-window condition, under unlimited visibility, in terms of situational awareness (SA) and mental workload compared to a head-down enhanced vision system. There were no differences between the 3 display concepts in terms of traffic spacing and distance and the pilot decision-making to land or go-around. For the KORD experiment, the visibility condition was not a factor in pilot's rating of clutter effects from symbology. Several concepts for enhanced implementations of an unlimited field-of-regard BTV concept for low-visibility surface operations were determined to be equivalent in pilot ratings of efficacy and usability.

  15. FutureGen 2.0 Monitoring Program: An Overview of the Monitoring Approach and Technologies Selected for Implementation

    DOE PAGESBeta

    Vermeul, Vince R.; Strickland, Chris E.; Thorne, Paul D.; Bjornstad, Bruce N.; Mackley, Rob D.; Kelly, Mark E.; Sullivan, Charlotte; Williams, Mark D.; Amonette, James E.; Downs, Janelle L.; et al

    2014-12-31

    The FutureGen 2.0 Project will design and build a first-of-its-kind, near-zero emissions coal-fueled power plant with carbon capture and storage (CCS). To assess storage site performance and meet the regulatory requirements of the Class VI Underground Injection Control (UIC) Program for CO2 Geologic Sequestration, the FutureGen 2.0 project will implement a suite of monitoring technologies designed to 1) evaluate CO2 mass balance and 2) detect any unforeseen loss in CO2 containment. The monitoring program will include direct monitoring of the injection stream and reservoir, and early-leak-detection monitoring directly above the primary confining zone. It will also implement an adaptive monitoringmore » strategy whereby monitoring results are continually evaluated and the monitoring network is modified as required, including the option to drill additional wells in out-years. Wells will be monitored for changes in CO2 concentration and formation pressure, and other geochemical/isotopic signatures that provide indication of CO2 or brine leakage. Indirect geophysical monitoring technologies that were selected for implementation include passive seismic, integrated surface deformation, time-lapse gravity, and pulsed neutron capture logging. Near-surface monitoring approaches that have been initiated include surficial aquifer and surface- water monitoring, soil-gas monitoring, atmospheric monitoring, and hyperspectral data acquisition for assessment of vegetation conditions. Initially, only the collection of baseline data sets is planned; the need for additional near- surface monitoring will be continually evaluated throughout the design and operational phases of the project, and selected approaches may be reinstituted if conditions warrant. Given the current conceptual understanding of the subsurface environment, early and appreciable impacts to near-surface environments are not expected.« less

  16. Evaluating the Suitability for CO2 Storage at the FutureGen 2.0 Site, Morgan County, Illinois, USA

    SciTech Connect

    Bonneville, Alain; Gilmore, Tyler J.; Sullivan, E. C.; Vermeul, Vincent R.; Kelley, Mark E.; White, Signe K.; Appriou, Delphine; Bjornstad, Bruce N.; Gerst, Jacqueline L.; Gupta, Neeraj; Horner, Jacob A.; McNeil, Caitlin; Moody, Mark A.; Rike, William M.; Spane, Frank A.; Thorne, Paul D.; Zeller, Evan R.; Zhang, Z. F.; Hoffman, Jeffrey; Humphreys, Kenneth K.

    2013-08-05

    FutureGen 2.0 site will be the first near-zero emission power plant with fully integrated long-term storage in a deep, non-potable saline aquifer in the United States. The proposed FutureGen 2.0 CO2 storage site is located in northeast Morgan County, Illinois, U.S.A., forty-eight kilometres from the Meredosia Energy Center where a large-scale oxy-combustion demonstration will be conducted. The demonstration will involve > 90% carbon capture, which will produce more than one million metric tons (MMT) of CO2 per year. The CO2 will be compressed at the power plant and transported via pipeline to the storage site. To examine CO2 storage potential of the site, a 1,467m characterization well (FGA#1) was completed in December 2011. The target reservoir for CO2 storage is the Mt. Simon Sandstone and Elmhurst Sandstone Member of the lower Eau Claire Formation for a combined thickness of 176 m. Confining beds of the overlying Lombard and Proviso Members (upper Eau Claire Formation) reach a thickness of 126 m. Characterization of the target injection zone and the overlying confining zone was based on wellbore data, cores, and geophysical logs, along with surface geophysical (2-D seismic profiles, magnetic and gravity), and structural data collected during the initial stage of the project . Based on this geological model, 3D simulations of CO2 injection and redistribution were conducted using STOMP-CO2, a multiphase flow and transport simulator. After this characterization stage, it appears that the injection site is a suitable geologic system for CO2 sequestration and that the injection zone is sufficient to receive up to 33 MMT of CO2 at a rate of 1.1 MMT/yr. GHGT-11 conference

  17. Fukuyoa paulensis gen. et sp. nov., a New Genus for the Globular Species of the Dinoflagellate Gambierdiscus (Dinophyceae)

    PubMed Central

    Gmez, Fernando; Qiu, Dajun; Lopes, Rubens M.; Lin, Senjie

    2015-01-01

    The marine epiphytic dinoflagellate Gambierdiscus is a toxicologically important genus responsible for ciguatera fish poisoning, the principal cause of non-bacterial illness associated with fish consumption. The genus currently contains species exhibiting either globular or anterior-posteriorly compressed morphologies with marked differences in cell shape and plate arrangement. Here we report a third globular, epiphytic and tychoplanktonic species from the coasts of Ubatuba, Brazil. The new species can be distinguished from G. yasumotoi and G. ruetzleri by its broader first apical plate that occupies a larger portion of the epitheca. Accordingly, phylogenetic trees from small subunit (SSU) and large subunit (LSU) ribosomal DNA sequences also showed strongly supported separation of the new species from the G. yasumotoi / G. ruetzleri group albeit with short distance. The molecular phylogenies, which included new sequences of the planktonic species Goniodoma polyedricum, further indicated that the globular species of Gambierdiscus formed a tight clade, clearly separated (with strong bootstrap support) from the clade of lenticular species including the type for Gambierdiscus. The morphological and molecular data in concert support the split of Gambierdiscus sensu lato into two genera. Gambierdiscus sensu stricto should be reserved for the species with lenticular shapes, highly compressed anterioposteriorly, with short-shank fishhook apical pore plate, large 2' plate, low and ascending cingular displacement, and pouch-like sulcal morphology. The new genus name Fukuyoa gen. nov. should be applied to the globular species, slightly laterally compressed, with long-shank fishhook apical pore plate, large 1' plate, greater and descending cingular displacement, and not pouch-like vertically-oriented sulcal morphology. Fukuyoa contains the new species Fukuyoa paulensis gen. et sp. nov., and F. yasumotoi comb. nov. and F. ruetzleri comb. nov. PMID:25831082

  18. The dismantling of Calliobothrium (Cestoda: Tetraphyllidea) with erection of Symcallio n. gen. and description of two new species.

    PubMed

    Bernot, James P; Caira, Janine N; Pickering, Maria

    2015-04-01

    This paper aims to resolve the dual composition of the triakid shark-hosted tetraphyllidean genus Calliobothrium--an issue that has been recognized for over a decade. As it stands, this genus includes a number of large species with laciniate proglottids, most of which bear 3 suckers at the anterior margin of each bothridium, but it also includes a number of species that lack proglottid laciniations and bear only a single sucker per bothridium, most of which are relatively small. Discovery of 2 new species, 1 of each form, parasitizing the whitespot smoothhound shark, Mustelus palumbes, off South Africa, prompted the first molecular analysis of the genus. Bayesian inference and maximum likelihood analyses of 28S rDNA (D1-D3) sequence data generated for specimens of both new species as well as of 2 known species of the laciniate form (Calliobothrium australis and Calliobothrium cf. verticillatum) and 3 known species of the non-laciniate form (Calliobothrium violae, Calliobothrium riseri, and Calliobothrium barbarae) confirmed the reciprocal monophyly of the 2 clades, supporting establishment of a new genus. Because the type of Calliobothrium, C. verticillatum, is of the laciniate form, Symcallio n. gen., with Symcallio peteri n. gen., n. sp., from M. palumbes described as its type, is established to house members of the non-laciniate clade. The 11 described species consistent with this form are transferred to the new genus. A new species of the laciniate clade, Calliobothrium euzeti n. sp., is described from M. palumbes, and a revised diagnosis of Calliobothrium is presented. PMID:25506725

  19. Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov.

    PubMed

    Yi, Hana; Schumann, Peter; Chun, Jongsik

    2007-01-01

    An actinobacterial strain containing demethylmenaquinone DMK-9(H(4)) as the diagnostic isoprenoid quinone was isolated from a tidal flat sediment sample, from South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2054(T) represents a distinct phyletic line within the suborder Micrococcineae of the order Actinomycetales. The closest phylogenetic neighbour was Cellulomonas fermentans, with 94.7 % 16S rRNA gene sequence similarity. The novel isolate was strictly aerobic and slightly halophilic, with optimum growth occurring in 2-4 % (w/v) NaCl. Cells were non-motile, non-sporulating and rod-shaped. The peptidoglycan type was of the A-type of cross-linkage. l-ornithine was the diamino acid and d-glutamate represented the N-terminus of the interpeptide bridge. The predominant fatty acids were anteiso-branched and straight-chain fatty acids. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and an unknown phospholipid. The menaquinone composition of C. fermentans was determined to be MK-10(H(4)), MK-9(H(4)) and MK-8(H(4)) in the ratio 56 : 2 : 1. On the basis of the polyphasic evidence presented in this study, it is proposed that strain JC2054(T) should be classified as representing a novel genus and species of the suborder Micrococcineae, with the name Demequina aestuarii gen. nov., sp. nov. The type strain is JC2054(T) (=IMSNU 14027(T)=KCTC 9919(T)=JCM 12123(T)). In addition, it was clear from the phylogenetic analysis and chemotaxonomic data that C. fermentans does not belong to the genus Cellulomonas or any other recognized genera. Therefore, C. fermentans should be reclassified as representing a novel genus, for which the name Actinotalea fermentans gen. nov., comb. nov. is proposed, with strain DSM 3133(T) (=ATCC 43279(T)=CFBP 4259(T)=CIP 103003(T)=NBRC 15517(T)=JCM 9966(T)=LMG 16154(T)) as the type strain. PMID:17220458

  20. Description of Niveispirillum fermenti gen. nov., sp. nov., isolated from a fermentor in Taiwan, transfer of Azospirillum irakense (1989) as Niveispirillum irakense comb. nov., and reclassification of Azospirillum amazonense (1983) as Nitrospirillum amazonense gen. nov.

    PubMed

    Lin, Shih-Yao; Hameed, Asif; Shen, Fo-Ting; Liu, You-Cheng; Hsu, Yi-Han; Shahina, Mariyam; Lai, Wei-An; Young, Chiu-Chung

    2014-06-01

    A taxonomic study was carried out on a novel aerobic bacterial strain (designated CC-LY736(T)) isolated from a fermentor in Taiwan. Cells of strain CC-LY736(T) were Gram-stain negative, spiral-shaped and motile by means of a monopolar flagellum. Strain CC-LY736(T) shared the greatest degree of 16S rRNA gene sequence similarity to Azospirillum irakense DSM 11586(T) (97.2%), Rhodocista centenaria JCM 21060(T) (96.3%) and Rhodocista pekingensis JCM 11669(T) (96.1%). The major fatty acids were C16:0, C16:1 ?5c, C19:0 cyclo ?8c, C18:1 ?7c/C18:1 ?6c, C16:0 3-OH and C18:1 2-OH. The predominant polar lipids included phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidyldimethylethanolamine and two unidentified glycolipids. The common major respiratory quinone was ubiquinone Q-10 and predominant polyamines were sym-homospermidine and putrescine. The DNA G+C content of strain CC-LY736(T) was 67.60.1mol%. During phylogenetic analysis, strain CC-LY736(T) formed a unique phyletic lineage associated with Rhodocista species. However, the combination of genetic, chemotaxonomic and physiological data clearly indicated that strain CC-LY736(T) was a novel representative of the family Rhodospirillaceae. Based on the polyphasic comparison, the name Niveispirillum fermenti gen. nov., sp. nov. is proposed; the type strain of the type species is CC-LY736(T) (=BCRC 80504(T)=LMG 27263(T)). In addition, the reclassifications of Azospirillum irakense as Niveispirillum irakense comb. nov. (type strain KBC1(T)=ATCC 51182(T)=BCRC 15764(T)=CIP 103311(T)), and Azospirillum amazonense as Nitrospirillum amazonense gen. nov., sp. nov. (type strain Am14(T)=ATCC 35119(T)=BCRC 14279(T)=DSM 3787(T)) are proposed based on the polyphasic taxonomic data obtained in this study. PMID:24771126